EDIT: Thinking about it, E minor is fairly common in phrygian scale (it's the tonic chord), however, phrygian, unlike dorian or myxolidian, which are used at least sometimes, is super rare -- its dominant chord, B dim, is dissonant, which kind of sucks.
Functional harmony kind of goes out the window once you stray from the major/minor modes anyway. You have to lean heavily on the root to maintain the tonality, or else the perceived key center tends to shift.
I think it's safe to say the effect of metal songs using phrygian is negligible.
(Also, songs are often written in one key, then transposed in the studio.)
I'm not sure why F would be more popular than D and A. One hypothesis would be that it has fewer accidentals; it's not a fun key for guitars, but many contemporary pop songs aren't guitar-driven anyway.