You have a lot to learn about how MC and it's library works. The things you describe is very logical why they happen, and some of it can be prevented.
1. You believe it's wrong that MC should not recognize the deleted files, and move them from the library. I strongly disagree. What happens if your network connection drop? What if you unplug the disk, what if the controller get screwed? All the files would be gone from the library. With the ADDITION of your last suggestion, not a thing would be rememberd by MC, because all traces is wiped clean. All those hours you used to find meta data for your movies or rating of your music is gone. No, this is NOT the way. I admit that a small option to the auto import could be useful. Where you can identify each folder as more dynamic and hazardous folder. BUT it is very few people that want to use MC in this way in my opinion, and would probably be a waste to add code for.
2. When you delete files, there is a hidden library that keeps a track on what things that have been deleted previously. IF you do not choose to ignore previously deleted files in the Auto import, you will end up with the files not being added again. This is just a user error, and not MC's fault.
3. This is where you expect things to be wiped clean toatlly when removeing things from the library. This CAN be done, but is is a very good safety thing for those that for instance accidentally delete files. If you ABSOLUTELY have to delete all, you can find the deleted files by using "a=~" or something like that, in the search box, and delete those again. Don't remember exactly the expression now.
4. You ask for a database tool. Why do you need that? You have very powerful tools, to rename, move, tag based on a LOT of criterias, mass edit fields, use custom expressions so you don't have to edit, and so on and so forth. A lot of us have ten thousands of media files on our servers or HTPC's, and those of us who know how to use this tools, never complain. Instead of complaining of missing tools, try to ask if what you want to do is possible with what we got in MC. I can almost guarantee you that it does.
5. Smartlists works as the library it self. If the file is deleted, or the disk is missing, the library does not remove the files. Because of this the tumbnails does not get deleted either. And thank god for that. I often play a series and add a custom thumbnail on it, because the ones I got are at a bad position in the series, or it just looks bad. If those got messed up each time my server goes down, there would be hell to pay
Your whole problem seems to be tied with the fact that you want to use media in very temporary directories with media being added and deleted all the time. If that is the case, perhaps you should use Explorer most of the time and just right click to issue commands in MC? Either that, or you can actually try to use some of MC's real strengths, add some views, panes and more columns so you can start using MC more effectively than explorer. If you can keep your jobs inside MC, all your troubles would go away.
I don't think this is the exact answers you want. But there is just not much more positive answers you will get I'm afraid.
