I used to index my NAS with the command line
mdutil -i on. Ok, I know it's not perfect, but it worked for me.
But since I updated to macOS Sierra it's not working anymore.
If I type
mdutil /Volumes/name -i on I just get the feedback
Indexing disabled. It doesn't matter if I use SMB or AFP (SMB was always working for me).
Maybe this information is helpful for a solution, if I
mdutil /Volumes/name -E I get the feedback:
mdutil disabling Spotlight: /Volumes/archiv -> kMDConfigSearchLevelFSSearchOnly. Indexing disabled.
Does anyone has any solution?