Hi,
Javascript is a complex topic.
1. All our extensions uses a javascript framework at some point. We first tried to rely as much as possible on mootools, which was the defacto js library on joomla as it was, and still is in joomla by default. So our extensions do not include it but load it from joomla and thus the mootools version varies based on the version of joomla.
We then started to use jquery as Joomla changed their main js library from mootools to jquery but as we needed backward compatiblity, we had to include jquery in Hikashop. We don't always load it (only when necessary), and the version varies as well based on the version of joomla you're using.
We also have our own javascript "library" that we started as we had too much issues with conflict with other extensions using improperly jquery/mootools on their end.
2. It depends. If everyone would use the mootools/jquery of joomla like we do, there would be way less js conflicts as joomla loads them only once per page. The fact is that most templates and extensions load their own version of mootools/jquery instead of using joomla's and thus you usually end up with several versions on the pages and that create conflicts.
Some try to mitigate these conflicts, but there is no real solution put forward yet.
3. There is such cache table, but not all extensions rely on it and there is not one sure way to avoid incompatibilities with the way it is done. Of course, there is no documentation that I know of published for joomla on that subject.
4. Yes, in the order it process the extensions. Normally, the current component is first processed, then the modules and then the template. The plugins are processed all over the place.
5. No. It's getting worse as the number of javascript libraries increase and the advent of new types of frameworks like bootstrap.
6. Yes, it is a real mess and I don't see a real solution emerging any time soon.