I think they are legitimate questions, and most of them have answers better than just "that's how Game Freak did it".
For example the Giratina one is asking about its role in the game, not why did GF make it. The Focus Band one was about a confusion in the way the Sash/Band work. The Splash one is a duplicate, but Splash seems like it's useless so the question is asking if there is a reason it would exist (i.e. is there an extra effect the person didn't know about).
That's not cause to start asking "Why does Bulbasaur exist" and so on for every Pokemon/move etc, because then the answer really just is "they wanted to make that Pokemon". But as long as they have a reason for asking the question I don't see a problem.