Just to elaborate further (didn't read the whole thread), War Mode also has special population rules. Every War Mode shard is either 50:50 balanced, or all Horde (because more Horde players tend to have WM on). If you're a player on the dominant faction, then there's a high chance that you'll be put on an "overflow" shard in War Mode and see significantly fewer people.
I wouldn't be surprised if War Mode shards also just have lower population targets overall, to keep it from becoming a completely unplayable bloodbath of PvP.