Sierra has made some changes, some of these may be to do with authentication or AFP or Time Machine or something else. This is almost always the case when Apple release a new version of the operating system.
Apple has not yet discontinued AFP but they have previously give a clear indication they intend to. Their previous comment on this subject went along the lines although these are not their exact words that -
- Everyone can use SMB,
- SMB is therefore the universal standard for all operating systems, not just Mac
- All servers - including real servers support SMB but most servers i.e. real servers do not support AFP
- SMB is faster than AFP (true)
- As only Mac users use AFP the amount of effort Apple has to put in to developing and maintaining AFP just for the benefit of a relatively small number of Mac users is increasingly hard to justify. This is on top of the effort Apple has to make writing their own SMB implementation as Apple no longer uses SAMBA
- Ergo we - Apple will phase out AFP in favour of SMB
So for the last few versions of OS X it has already been the case that the Finder will try and use SMB instead of AFP if possible, this remains the case with Sierra.
What has changed is that for the very first time Server.app 5.2 on Sierra can share a volume for use as a network Time Machine destination via SMB! This is something I suggested to Apple myself a couple of years ago after their above comments about AFP, clearly if Apple intend to stop providing AFP at some point they need to change Time Machine to match.
Now that Apple have updated their Server.app Time Machine to support SMB, one can expect either Time Capsule to be similarly updated or replaced or discontinued. Once this is done it maybe that the next macOS upgrade will remove all AFP support, or at least make it invisible and inaccessible to normal users like NFS.
At this point in time I am not aware of it being possible to use any third-party SMB file servers for Time Machine backups. I would expect the SAMBA team to add this feature over the next few months.
Note: Nearly all NAS servers use SAMBA for SMB sharing, and another open-source project called Netatalk for AFP sharing, this includes Synology and Netgear/ReadyNAS.
Note: Apple do not officially support third-party NAS devices. Well duh! Apple don't make them so why should they? This does not mean such devices cannot work. I also use a ReadyNAS as a Time Machine system. I don't expect Apple to help me out if I have a problem with it.
If or more accurately when Apple release a new version of their operating system and it (again) breaks things then the usual pattern is to wait for the relevant open-source project team i.e. Netatalk for AFP to work out what changed and for them to update their software to match. Then there is a further wait for the NAS maker to take the new version of Netatalk and to add it to their own software. Historically Netgear i.e. ReadyNAS were very good at this because they were a top tier contributor themselves to the Netatalk project. I am sadly not as convinced of their speed anymore especially with regards to the now very old 4.x firmware models, current models use 6.x firmware.
For those having AFP problems with NAS devices you need to differentiate between whether it is a complete AFP failure or just a Time Machine failure. You should also double-check your NAS firmware is up-to-date and I can confirm that 4.2.28 is the current version of firmware for that (old) generation of NAS.
Now saying all the above, it remains a potential possibility that this is not actually a deliberate change by Apple but an accidental bug. So, there would be no harm reporting it as such. Apple may respond with their infamous 'works as designed' answer in which case we wait for the Netatalk team to fix it their end.
PS. Both the SAMBA team and the Netatalk teams have added Spotlight support to their software. Sadly many NAS makers have yet to make these features accessible on their NAS boxes. It would be possible to do this on a DIY Linux server.