"Who are you looking for?"
I think it might be related to context! You see someone crawling around you might as well ask What are you looking for? As it's an obvious continuous action you are probably going to use 在 in this situation!
On the other hand, a secretary might use "你找谁" when you come in, without 在, because it seems to be a point action: you come in and ask, period!
I might be wrong but that's my reasoning for now!
Maybe a more direct translation could be "Who do you look for?" But that doesn't sound natural for me!
If you used "whom" here, you couldn't also use "for" at the end. But yeah, the correct English would be "For whom are you looking?" Sounds weird, though, as nobody uses that anymore. Language evolution! Yay!
You are right, but it's even more used who, specially in an informal situation.
But I agree that whom is more grammatically correct.