mp3s set as "Audiobook" have stopped showing up in iBooks
If I am understanding you correctly, you have MP3s which are audiobooks which exist in iTunes on a desktop/laptop and you want them to sync to a mobile device and be automatically available in iBooks the way they used to be, is that right?

Apple recently changed the way audiobooks sync between iBooks and iTunes. This support document lets you know how you can sync these files using iCloud which seems to be the way they are encouraging people to do this sort of thing now. In short


iBooks must be turned on in iCloud settings on your Mac and your device
in iBook's general preferences you have to makes sure "Sync bookmarks, highlights and collections across devices" is checked
Make sure you don't have "Hide iCloud Books" selected from within whatever Collection you are viewing in iBooks


And then when you sync you should see these files as "downloadable from the cloud" (i.e. with the little cloud icon next to them) and then you can tap to download.

I think this is sort of a nutty workaround for what used to just work but seems to be how Apple is trying to get people to do what you are tying to do here.