FontNuke doesn't delete fonts, it deletes font cache data. All of your fonts are still on the drive. What's wrong is Font Book's database is corrupt. Or at least, 99% of the time, that's what's wrong when the fonts are listed in Font Book, but none, or only some of them appear in your apps.
Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding the Shift key until you see a progress bar towards the bottom of the screen. You can let go of the Shift key at that point. Yosemite is a bit different. Whether it's a Safe Mode boot or a normal one, you get the same progress bar. It just takes longer to get to the desktop in Safe Mode. So hold the Shift key until you get to the desktop.
OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally. This will clear Font Book's database and the cache files of the user account you logged into in Safe Mode.