it is similar to ground loop/high noise floor:
the fans are going at a constant 'tone'-- or they are always pushing 'x' amount of air-- similar to what the whine of a ground loop does.
as soon as you turn up the music, you temporarily overpower the constant 'tone' of the fans, but they are still continuously there. same as the ground loop-- the noise is always there even when you turn it up.
so while the subs 'beat' might momentarily disrupt the air flow, i don't think it would disturb the overall airflow that the fans are creating.
i ran a fan directly on top of one of my old sub amp(before i blew it up in a unrelated issue)-- it seemed to help, though i was too young to actually take temp readings to prove it..