DeathToDSStore [2] works as well, but like Asepsis it requires you to disable SIP, and that's very much not recommended!
I wonder if its possible to hook into Spotlight real-time (with mdfind?) and just delete them right after its created. Together with disabling it on networks that should be "good enough" to not see them. Might be problematic with removeable media such as USB sticks though. If you're sync/unmounting those via command line, consider a find with xargs [3] on that media before unmounting.
I haven't looked at Blue Harvest as already suggested. If that still works (without disabling SIP) I'm curious how they do that.
[1] defaults write com.apple.desktopservices DSDontWriteNetworkStores true
[2] https://github.com/snielsen/DeathToDSStore
[3] find /path_to_USB_media -name .DS_Store -print0 | xargs -0 rm
Not Spotlight but the File System Events API, which was designed for precisely this kind of thing.
There was (is?) a configuration that stops it for network paths, and 10.10 used to have aseptic (a kext that redirected those) but as far as I know there was no way in 10.11 or 10.13