2. Houhnynhmmnmnmnnms, or whatever that word was Swift made up; Gulliver from Gulliver's travels was a member of the League at one point, and in one of his travels, he meets a country full of talking horses with a collection of consonants that would make H.P. Lovecraft go "too much" for a name. He even tries to become a citizen of this country (making him the original brony in this world), but is eventually kicked out for not being a talking horse. At the very least, this is the explanation for "earth ponies;" (apparently, they got over their love of unpronounceable names at some point); Equestria being the modern day equivalent of this horsey country from older sources would be inside the League wheelhouse.
The Christmas episode about the founding of Equestria would probably account for the unicorns and pegasus; I know there was a unicorn that sung referenced in Vol. II and "The Black Dossier" (it's actually a really dirty, smutty reference, and funny as hell in the "Black Dossier" callback). Pegasi, talking or otherwise, are never mentioned that I can recall, at least until the Wonderbolts poster, but that's not a big deal; there are plenty of fictional pegasi, talking or otherwise, obviously. Equestria, in the League universe, would be a country founded by an alliance of intelligent equine races. Heck, it's probably part of the United Nations; however, I am not aware of any other non-human races with their own country. But, given the prominence of Gulliver in the League's history, it's the most likely explanation.
3. Alternate, or perhaps more accurately, overlapping universes do play a big part of the League world; eventually, the League is based in the "Blazing World," where a lot of weird things exist that otherwise wouldn't fit in with the world of the League. However, I don't think the Equestria Girls "mirror universe" would be the League explanation, mostly because Equestria Girls didn't come out until a year after the book was published. Furthermore, "mirror" universes in the League world are secretive; they wouldn't be crossing over and advertising flying shows.
4. I doubt any future League comics will ever directly deal with the ponies, though the Houhynmmnnmnmmnmnmns may appear in a comic dealing with Gulliver's team, and there may be hints about that they will eventually become the ponies of Equestria, but that's about it. They couldn't directly involve the characters, no, because, of copyright issues; most League characters are public domain, after all. A quick reference is one thing; a comic dealing with the League of Extraordinary Gentlemen fighting Discord with the help of Twilight Sparkle and friends is something else entirely (and I think Alan Moore would kill himself before writing that, anyway). That's the League comics modus operandi; they make vague references, they don't spell it out. Also, seeing as how the 2009 comic was pretty much Moore dumping on modern popular culture, there is no reason to believe that either Moore or O'Neill actually think very highly of MLP:FiM. But more on that in part 5 ...
5. Reasons the poster was changed? Maybe they were afraid of copyright, again (I doubt they'd get in trouble with the show that allows everyone and their dog to upload episodes to YouTube, but maybe they got cold feet). Unlike other things referenced, I would not be surprised if "WonderBolts" and their symbol is actually a trademark of Hasbro; due to the modern setting, they almost certainly had someone go over it to make sure nothing trademarked was actually used, and probably the WonderBolts were brought up.
Alternatively, one or the other decided, after the page was drawn, you know what, screw that. We're not doing ponies. I could see that. And finally, possible in story reason, most of the other posters on that page are for musical groups, and also very adult oriented; perhaps they just decided that if a group of ponies were going to put on a flight show for humans and sell tickets, they would probably advertise somewhere more family oriented, as that would be their audience; realistically, the WonderBolts and "Niggas With Hats" wouldn't be advertising in the same area. They may have just decided the "ASS id Attack" reference (nobody gets) was more "in character" for the panel.
6. I specifically pointed out "Cupcakes" and the lot; dark fanworks are prevalent. My point wasn't "bronies wouldn't like whatever he does dark to them," my point was, if Moore wants to be shocking, he's got his work cut out for him. I seriously doubt Moore cares about what League fans think about what he's doing, nevermind bronies. Actually, that'd probably be it; the dark twist would be bronies, except in this world, they are humans who want to, like Gulliver, become citizens of Equestria.
And then there'd be a panel implying somebody screwing a pony.
1. Sombra sucked.
2. Houhnynhmmnmnmnnms, or whatever that word was Swift made up; Gulliver from Gulliver's travels was a member of the League at one point, and in one of his travels, he meets a country full of talking horses with a collection of consonants that would make H.P. Lovecraft go "too much" for a name. He even tries to become a citizen of this country (making him the original brony in this world), but is eventually kicked out for not being a talking horse. At the very least, this is the explanation for "earth ponies;" (apparently, they got over their love of unpronounceable names at some point); Equestria being the modern day equivalent of this horsey country from older sources would be inside the League wheelhouse.
The Christmas episode about the founding of Equestria would probably account for the unicorns and pegasus; I know there was a unicorn that sung referenced in Vol. II and "The Black Dossier" (it's actually a really dirty, smutty reference, and funny as hell in the "Black Dossier" callback). Pegasi, talking or otherwise, are never mentioned that I can recall, at least until the Wonderbolts poster, but that's not a big deal; there are plenty of fictional pegasi, talking or otherwise, obviously. Equestria, in the League universe, would be a country founded by an alliance of intelligent equine races. Heck, it's probably part of the United Nations; however, I am not aware of any other non-human races with their own country. But, given the prominence of Gulliver in the League's history, it's the most likely explanation.
3. Alternate, or perhaps more accurately, overlapping universes do play a big part of the League world; eventually, the League is based in the "Blazing World," where a lot of weird things exist that otherwise wouldn't fit in with the world of the League. However, I don't think the Equestria Girls "mirror universe" would be the League explanation, mostly because Equestria Girls didn't come out until a year after the book was published. Furthermore, "mirror" universes in the League world are secretive; they wouldn't be crossing over and advertising flying shows.
4. I doubt any future League comics will ever directly deal with the ponies, though the Houhynmmnnmnmmnmnmns may appear in a comic dealing with Gulliver's team, and there may be hints about that they will eventually become the ponies of Equestria, but that's about it. They couldn't directly involve the characters, no, because, of copyright issues; most League characters are public domain, after all. A quick reference is one thing; a comic dealing with the League of Extraordinary Gentlemen fighting Discord with the help of Twilight Sparkle and friends is something else entirely (and I think Alan Moore would kill himself before writing that, anyway). That's the League comics modus operandi; they make vague references, they don't spell it out. Also, seeing as how the 2009 comic was pretty much Moore dumping on modern popular culture, there is no reason to believe that either Moore or O'Neill actually think very highly of MLP:FiM. But more on that in part 5 ...
5. Reasons the poster was changed? Maybe they were afraid of copyright, again (I doubt they'd get in trouble with the show that allows everyone and their dog to upload episodes to YouTube, but maybe they got cold feet). Unlike other things referenced, I would not be surprised if "WonderBolts" and their symbol is actually a trademark of Hasbro; due to the modern setting, they almost certainly had someone go over it to make sure nothing trademarked was actually used, and probably the WonderBolts were brought up.
Alternatively, one or the other decided, after the page was drawn, you know what, screw that. We're not doing ponies. I could see that. And finally, possible in story reason, most of the other posters on that page are for musical groups, and also very adult oriented; perhaps they just decided that if a group of ponies were going to put on a flight show for humans and sell tickets, they would probably advertise somewhere more family oriented, as that would be their audience; realistically, the WonderBolts and "Niggas With Hats" wouldn't be advertising in the same area. They may have just decided the "ASS id Attack" reference (nobody gets) was more "in character" for the panel.
6. I specifically pointed out "Cupcakes" and the lot; dark fanworks are prevalent. My point wasn't "bronies wouldn't like whatever he does dark to them," my point was, if Moore wants to be shocking, he's got his work cut out for him. I seriously doubt Moore cares about what League fans think about what he's doing, nevermind bronies. Actually, that'd probably be it; the dark twist would be bronies, except in this world, they are humans who want to, like Gulliver, become citizens of Equestria.
And then there'd be a panel implying somebody screwing a pony.