In my case, only the All Fonts and Gaeilge libraries were left, both empty. Trying to add more fonts had no effect, until I eventually realised I had to create a new library as a workaround and add fonts to that.
This worked, although due to the aforementioned .CFUserTextEncoding problem I had to open Font Book every login before applications that used interesting fonts, or they wouldn't find any.
Just for the sake of it, I opened up a bug report with Apple, not really expecting to hear anything back. A few weeks later though, I did hear back from them, with a solution that worked:
"Look for a directory called: com.apple.ATS inside of /var/folders
Once you find it, copy this directory to another location and then remove it."
Doing this and rebooting the MacBook, I logged in again and started Font Book to find, lo and behold (drumroll and angel choir) that the User and Computer font libraries were automatically added again and all the fonts loaded back into them. BRILLIANT, thanks Apple, I totally didn't expect that. Thumbs up from me!