sadly, they remove all them from all the flying fortress on the dragon knight saga one in each area. i personally think that was big mistake to do...having them made the areas seem like a huge puzzle to solve. your right the fortesses seemed dead without life even though there was pently to fight. they also removed the chest with the armor in them too...it was fun and exciting to search for those armor sets (to see if you could find every single piece). like huge treasure hunt. other words the fortesses became boring on the outside after destroying the nest/balllistas/wizars tower.
besides that as a whole i really loved this game a lot, just think if they left some of the stuff that was in the orginally ddII in, it would had made it even better.