Batman's final "Where is it?" bit is funny, but not in a bad way. It's still a powerful moment. Maybe it's because most of us have forgiven the bat-voice to begin with. But it shows how exhausted Batman has become, but how furious he is. It tells a lot.
The voice is funny, but I don't really feel it takes away from the scene at all. It's funnier because he has a moment like that in each film so it feels like a little bit of an homage. I think it's "Where is it?" in BB and "Where are they?" in TDK.
At any rate, while my friends and I like repeating the "WHERE IS IT?!!" Bat-voice for fun, I don't think it takes away from the scene at all.
EDIT: The only part of this movie that I find just sort of poorly done was Tate's death scene. It was a little distracting how comically she died, but meh, out of 3 hours of wild and intense fun I can accept a cheesy minor character's death.