MC is pretty good at figuring out what files have disappeared. It's also pretty great at importing those same files when you put them into a new location.
But you should be aware that moving files externally is NOT AT ALL like moving them inside of MC. When you move files using MC, it knows what's going on and it preserves all of the attributes including IMPORT DATE.
When you move externally, MC deletes the records for the files. Then it re-imports them. So, if you aren't writing every single tag to the files, you will lose any tagging changes you have made. The IMPORT DATE will also change because MC considers it a brand new file.
If you are detailed about your library and it's properties, do not move files externally. Always use RM&C to move files or "update database location". Turn off auto import. Turn off fix broken links.
This changes will have MC properly track all files. You will know when auto import runs (because you run it yourself). You will be able to see what happens with each auto import and verify that it did what you wanted it to do. You will never lose track of files that are temporarily unavailable. In short, you will have full control.
On the other hand, if you are more casual about your library, import dates, tags, etc.... then letting MC do it all automatically is pretty decent. You can decide based on your own desires.
Good luck.
Brian.