I don’t think there is much overhead. MFS just manages references in a DAG, it does not copy blocks around. Of course an update in a leave on a 1000-level deep MFS DAG may lag a bit.
No, you need to put it on MFS after you do your regular add. That way you can give a name to what you added (and modify the content as needed). See ipfs files --help for info about MFS in general.
ipfs add --nocopy -r /root/.ipfs/nas/folder1/shared_folder and get the e.g. Qm1234567...
ipfs files cp ipfs/Qm1234567...... /shared_folder
Now I cannot forget the root folder’s Qm... because I always can run: ipfs files stat /shared_folder
which gives me the Qm... of root folder.
Also I can run: ipfs files stat /shared_folder/a_file_or_folder
to get the corresponding Qm...