There's no way to tell. If i had to guess I'd say there is constantly at least 10-20 AFKers > 1 hour though sitting in the tower. I've seen PK1 sit AFK for 3 days before. 
Total or per side? Either way, 300-400 in an arena and 3-10 per side AFK? Really going to make that much of a difference? Even if they are booted to "make room" in the arena vis a vi the cap, wouldn't the cap change correspondingly and not make a difference either?
There have been instances, using bish as an example, where we had so many logged in but you can easily look at the map and notice that bish had nowhere near the amount of dar as there should be with those numbers, were they in GV's on the ground? Not all, as you select there names and "goto" you can find them in towers nowhere near a fight and not responding or flying for hours, there have been several instances of people AFK with cv's for hours at a time and if you dont have a score to take control of it, its a loss to everyone that could have used it.
You will usually see alot of this just before a reset on any side, people switch over and AFK for the perks, or even worse log in AFK overnight just to maintain ENY on a side. Seen it all, A timer would resolve all that easily.
The CV thing. Bug? There was a CV the other night that no one could take control of. But hey, maybe it's SPIEZ!1!!.
AFK for perks? I guess they don't know that this doesn't work? Isn't it 24 hours on a side minimum to get "win teh war" perks? Couldn't you get as many, if not more perks flying an hour for the low number side? Couldn't you make as many or more perks by switching to the "losing" side? Educate the masses.
AFK to maintain ENY? Really? More than one, no more than five people, per side, will actually plan to maintain ENY by going AFK for an extended amount of time? You really believe this? I would have to

their dedication and foresight as silly as it seems.
wrongway