In my experience you can tell where the special forces are hanging out, but it takes a lot of staring at the galactic map. In most of my games there are only three sources of moving ship blobs: Exowaves, which are clearly announced and easily distinguished; threat, which is explicitly labeled as such on the galactic map with the right filter; and the special forces. So to find the SF, just look for the moving blob of non-threat ships.
It might be different with more minor factions on (hybrid hives or dark spire perhaps which would add more non-threat movement) but in my experience since I can usually *roughly* tell where the special forces are currently holed up, it would just be a timesaver to have them identifiable via a map filter just like threat currently is. And like threat, there's no need to have individual ships ID'd, a map filter is plenty.