Hey Michael,
1. Yes & no. There is no such as different maps. You can specify different categories and put hotspots in this category. Then for each category you could create a menu link and have the system load just the hotspots from this category. And for example hide the filters all together on the page. This way people will only see hotspots from the categories you've specified in the menu.
2. You can use the content plugin to link to a single hotspot or to use the hotspotsanywhere plugin to link to the whole component
3. No idea. Hotspots is build with bootstrap and few js libraries. If JSN EPIC PRO doesn't create any js errors (or any other plugin, module or component) than hotspots will work as expected.
Regards,
Daniel