You ask good questions. I can give you my thoughts, and maybe others can give theirs.
I have not upgraded my Moodle 4.5. I have a brand new Moodle 5, and I am redoing my courses and question bank. Here is what I have observed:
If I backup/restore a Moodle 4.5 course that had questions in the System, Category, Course, and levels, these come into a Moodle 5 course-level question bank named "System shared question bank." The question categories are quite nicely organized, just like they were in Moodle 4.5. This "System shared question bank" is "owned" by the teachers in this course. Any teacher in this course can use questions from the "System shared question bank" in any other course that they teach. So you haven't given up anything, and perhaps your teachers now have an easier way to share questions.
However, the problem is that for every course that was using Moodle 4.5 "Category" and "System" banks, all questions are also repeated in every course. So you probably end up with a lot of repeated questions, and you somewhat might lose the concept of a "common" question that when edited, everyone will see. This is where some extra effort will have to be invested, from how I see it.
(You mention two shared banks showing. Perhaps this is what happens when Moodle 4.5 is upgraded to Moodle 5. I don't know.)
So, you can designate one course as the "Master." However, other courses will then need to edit their quizzes and link back to the Master Course questions, if you desire to retain "common" questions. Yep, some effort, but then some better sharing. And in the long run, this might be best. In the short run, it might create some confusion.
So, a lot of one's strategy will depend on where you want to end up, and how much effort you want to invest.
Here is what I am doing (since you kinda asked.)
I began with a brand new Moodle 5, and configured it according to my notes about how I customized Moodle 4. Then, I imported questions from Moodle 4.5 into Moodle 5, a "Master Course" and made sure to carefully organize them into sub-categories. I backed up my Moodle 4.5 courses, without users, and without questions, then restored these in Moodle 5. These restored courses do not contain quizzes when restored, so I am adding the quizzes back into them, and re-adding questions into each quiz by using questions from the Master Course. Even though I am my Moodle's administrator, what I am doing is what a typical teacher might do. This process might take me around 8 hours per course (I am not finished, yet). I have around four courses to worry about (i.e., to teach). But, I am in it for the long run, so I can accept this "time" investment. And it allows me to rethink and clean up my question bank. However, I suspect that many teachers would complain.