Notification functionality should be restored and working properly now. Have fun.
The resolution was bumping the code to v3.2.1 release, which appears to not have caused any ill effects. We may have to rollback if there are any significant issues, but the release was only 18 days ago.
@LovelessLiddell Thanks for letting me know. I patched the notification system to be compatible with the new schema until we get the 'follow user' feature which is what broke API access to your notifications. This is in line with issues I'd expect to see given the situation.
A server, for mew.