You want a guarantee? Then back up your iPad, early and often. The process appears to be a lot quicker, and much less painful, in the new OS.
You will eventually have to get your brain around the idea that the iPad simply is not a "MacBook Lite"; it has no Finder or other file-handling system which exists outside the various apps and doesn't have the flexibility which you're looking for.
The reason you don't see anything relating to your various bookmarks is that they will exist on your main system nowhere except in your backup file. If you want to pull them out then you'll have to play around inside that file itself, but I have no idea if you'll find anything recognizable or usable.
A short-term solution might be to see whether any of the other browsers handle bookmark storage better than the stripped Safari we now have; if so, you could eventually get switched over to using that. Longer term, perhaps requests to Apple, via the iPad feedback forms, to improve how Safari handles them could pay some dividends.