Just because forces took off from Ebou Dar and elsewhere does not mean that they were all invovled in the raid. Given the distances I could be wrong but I don't think they could fly there in one hop. That means they would have to set up a staging area somehere west of Tar Valon in the big empty grassland.

That would require some supplys be brough in, food for the soldiers, damane, sul'dam not to mention the raken and to'raken. They probably travelled light but if you take any modern army there will be a lot more soldiers at the base dealing with logistics that are actually going into battle. That might account for the numbers.

As for Egwene's observations she could not see the entire area, only out of the hole in the wall and what was in front of her. In the middle of a battle I could see someone getting confused and the numbers flying around the tower could be counted twice or more etc. She can probably give an accurate count of the flyers she downed but what if a to'raken flys past her, goes around the tower to some other point out of Egwene's view and after dropping off some soliders takes off and circles the tower back into Egwene's view. I doubt if she could, in the middle of a battle, say "oh that is the to'raken I saw a few minutes ago, I recognise its face." Instead it becomes another flyer.