I notice that both "hippo" and "hippopotamus" have the "species" category assigned to them, but the latter is...somewhat underrepresented in the database. Would it be worth aliasing things one way or the other?

I'd say alias to hippo.
It's technically more of a nickname, but it's the more commonly used name.

I'd say hippopotamus, because when tagging and searching, you can still look up hippo if it's aliased, but hippopotamus is more correct, and I'd be safe to assume that people know that hippo is just short for hippopotamus.