I think the tadpole storyline is going to culminate around the end of Act 1; I don't think it's going to have an arching storyline across the whole game. Whether you keep it in or not, I think it's going to have lasting effects like no sunlight sensitivity to those that would normally have it (drow, Astarion, etc). I think it's a great way to introduce the antagonists and giving us a reason for hunting them down...if illithids are the main protagonist of the whole game.
