Thanks for the invaluable advice Tim, I've been busy checking what happens on the scan via the shh terminal session on my Macbook. It really is quite a busy process and very helpful to see what causes any delays. I never realised I had 'opus' files in my collection which, I think, are seen as video content. I'm going to re-rip these as flac I think to prevent any delays. My m4a files are given a going over with 'ffmpeg' which takes a little time compared to general wav or flac files.
Wav files seem to sound cleaner than flac anyway, but to be fair, I have to do more listening to confirm this.

I still have a stall on the USB HDD and on my NAS file (nfs) server when running the scan, the process just stops but not at the end of the collection. I am going back to basics and only starting with my 'pure' ripped wav cd's as a collection then gradually add albums to get a better picture to what the problem is. Using ssh into the Pi3 is vital to see what's going on.

BTW the only way I could get the NAS working as a NFS share, because CIFS/SMB would'nt ever work was to create then add a file in the etc folder on the NAS server called 'exports' with the line '/media/hdd/Music 192.168.0.0/24(rw,no_root_squash,sync,no_subtree_check)' then it worked. The path shown at the beginning of the line has to match where your collection is located. My server is actually a VUsolo2 satellite media box running enigma 2 linux so that might be why? Still can't get CIFS/SMB to work on my other NAS server which is a Netgear Nighthawk X4 R7500 router, there's no password required but I get 'no password' error on trying to create a share.

Finally, Is there a way to backup your database once it's complete to a Mac or PC via the terminal then restore it, it's just that I find sometimes when the whole process has come to an end I might have a freeze then the database seems to have disappeared on reboot and I have to go over the whole thing again?