I have a sort of same problem concerning scanning the library. I have moved over my mt-daapd machine some mp3 using samba. I then deleted them but i have still on my itunes some of the songs that i have previously deleted. I stopped mt-daapd and then restarted it but it doesn’t seem to work.
If you don’t have background scans turned on, then it won’t notice that the files have changed. Also, the nightlies now don’t scan at startup, so that it can advertise faster.
So you can run with -s to force a scan at startup, or you can use the web interface (http://server:port, login as any user, using the admin_pw as a password), and hit the “Scan” button on the status page.