At first I was kind of annoyed by Shirahoshi being this special once-in-a-forever wonder, but just now I remembered all their talk about mermen/fishmen having the ability to give birds to completely unrelated mermen/fishmen through some ancient DNA or something. So it makes a whole lot more sense to me now. Pretty masterfully played.
Y'know when you put it that way, Hodi is kind of the prime candidate.
The most hard-hitting real life assassinations are those that come from inside issues (it was a religious jewish person who killed the most peace-pursuing Israeli prime minister, there are tons of other examples that hit real deep to people). Hodi is "inside" and it's incredibly ironic if he's the one to kill her. He's one of the people she's having in her mind, and there he goes and ends it. And let's not forget Hodi is also one of those kids Otohime spent her utmost importance on.
If we're talking about deep problems, Hodi is probably the most "fitting" person to kill Otohime. The outsiders were against the fishmen anyway, so what's so special about them assassinating their queen?
But yeah I agree this arc is trying to hit deep in a lot of places.