I just fiddled around with my setup again and found out that if I add new files to the library (SMB share) on the Windows side MMW instantly recognizes them. MMW only does not get informed if I add them on the Linux side.
I'm not sure, but it might be a known issue that SMB and inotify do not work properly together: https://stackoverflow.com/questions/812 ... t-in-linux
So, as you said, it is not the fault of MMW.

MediaMonkey relies on the system to inform it that there have been changes. This is not always done for network locations. Your setup adds even more complexity to this.

You'll likely have to run manual scans instead.

Since a few weeks I run MMW in a virtual machine (Windows 8.1) and the host OS is Debian.
My music files and the MM.db are now stored on a SMB network share.
Nearly everything seems to work quite stable.
I configured MMW to permanently monitor the SMB share for recently added new music. (don't know how this option is called in the GUI in English)
Unfortunately MMW doesn't recognize if I add a new song. My current workaround is to disable and re-enable the monitoring option. But then the whole share is scanned again which takes quite long.