You’re over-analyzing this imo. What’s probably happening is all the decent Horde players are probably asleep by 1-3 AM, leaving more no-lifers and under-geared alts in the pool of players.
The real question is, what are some Alliance players doing up queueing random bgs at 2-4 AM? Most normal people have jobs, lives, etc and are not up playing WoW at such unusual times.
The most simple explanation is the most likely one, no need to over-complicate it/write a book.