I'm going to assume that's more of a budget thing; the animation is really great, but water is notoriously hard to animate, and it's still a relatively small studio behind the movie, so they probably just decided, yeah, the story's not actually about boats and shipping, so we can assume that's all happening just off screen.
I'd say there are plenty of implications that the ponies use boats just in the setting. I mean, besides the lighthouse there is the literal name of earth pony's town being a horsey pun on the word "maritime", which does strongly imply the ponies use shipping. Also, there's not much reason else to have a city in a bay if shipping isn't involved somehow. Plus, the unicorns and pegasi negatively stereotype the earth ponies as smelling fishy, which implies an active fishing industry, of all things. (I think there's a pony parody of Lovecraft's "Shadow over Innsmouth" using seaponies fanfic prompt here.)
I'm going to assume that's more of a budget thing; the animation is really great, but water is notoriously hard to animate, and it's still a relatively small studio behind the movie, so they probably just decided, yeah, the story's not actually about boats and shipping, so we can assume that's all happening just off screen.
I'd say there are plenty of implications that the ponies use boats just in the setting. I mean, besides the lighthouse there is the literal name of earth pony's town being a horsey pun on the word "maritime", which does strongly imply the ponies use shipping. Also, there's not much reason else to have a city in a bay if shipping isn't involved somehow. Plus, the unicorns and pegasi negatively stereotype the earth ponies as smelling fishy, which implies an active fishing industry, of all things. (I think there's a pony parody of Lovecraft's "Shadow over Innsmouth" using seaponies fanfic prompt here.)