I'm not an expert by any means but I think I may be able to help some.
For your initial issue, I'm not sure what could causing that. Maybe try clearing your localthumbcache file and see if that helps.
1. Yes you can install poses in their own folder but as with all script mods, you can't go more than 1 folder deep. Meaning you can have a scripts folder but inside that folder, you can't have separate folders. With package files, you can go as deep as you want.
2. I would suggest keeping all files for specific mods in the same folder. I keep my scripts with my packages when they're part of the same mod. But as long as the script mods aren't more than one folder deep, you can organize them how you like.
3. I'm not sure either. I'm relatively new to poses and pose player as well.
4. The ones I've used, you don't have to have every space filled but it does make some pictures look weird. It depends on how the sims are posing. If you have a family photo with an adult holding a toddler but no toddler, the adult will still pose as if they're holding a toddler.
I hope this helps.