The vacuumed bees...can you tell how lively they are when you put them into the hive? Vacuums are notoriously hard on bees, at least for a while until you get it set up right. My first try with mine made the poor little bees (I tested on about 10 or 20 first!!) look like they went through a blender
Don't feel bad about losing a hive. You're gaining valuable information, saving some of the bees at least, and if you didn't the apartment complex would have emptied 20 bottles of raid in there anyway.
It sounds to me like they may have swarmed a week or 3 before, and the new queen hadn't had a chance to get set up very well yet. So you wouldn't find a big fat queen, young brood, or queen cells.