Thanks for the replies, much appreciated.
I've done a bit of experimenting and it seems that the nc_id's remain constant unless the table is wiped by myself, so I'll just have to remember to back up Anope's mysql database rather than let Anope repopulate it by itself if I ever move servers or something.
I've been able to get passwords to match by using md5('whatever', true) in PHP and LEFT(pass, 16) in mysql, it's a little messy but it does the job.