Well, first of all, I'm sorry to hear you're running into issues, and happy to hear you like the application.
I do have a question though, since indexing my shares never worked on my Mac, no matter how I mount my shares (Finder, Terminal, CMN etc).
So my question would be: how do you manually mount a share and get it indexed? I mean this as a serious question: since it's something I run into often as well.
Having said that: CMN mounts either with the official Apple API (which Finder would use as well), or in Commandline mode (if you set it like so, which would be the manual mount method one would use in Terminal).
I guess the best way to see if there is something different, we could comparing the "mount" output in Terminal. Maybe that could give away a hint on what may be going on.
1. Mount your share manual, as you described, and post the "mount" out here. (feel free to copy only the relevant line)
2. Unmount the share, and now mount it with Automounter, and see what the "mount" output is.
3. Unmount again, and now mount it with CMN, and see what the "mount" output is.
The output lines you're looking for:
//username@servername/pathname on /path/where/itsmounted (smbfs, nodev, nosuid, mounted by username)
As far as I know, indexing network shares is a little iffy since (if I recall correctly) macOS Monterey (or earlier).
You can tell Spotlight to index a volume, but for me this never worked in a reliable way. You can force Spotlight to index a drive like shown below. If this works for you, than I can maybe add this as a CMN option 😊
Enable indexing in a share (where /Volumes/MyNASShare is the directory where the share is mounted);
sudo mdutil /Volumes/MyNASShare -i on
Please let me know if this helps as well, as it could be a helpful function to add to CMN. I'm running another test on my NAS as we speak, but it takes a while to finish indexing.