I put EM on my GEVs, reasoning that populations usually seem to have higher EM signatures.
Correct
Converseley I use thermals on my GSVs as they are more likely to be around ships in open space so thermals are a better guarantee for detection.
Correct
Would you always try and have both?
I always have size 1 EM, TH and Active in ALL ships. On commercial vessels it helps with detection of enemies and general contact tracing, in war ships they act as back up shall leaders or scouts be suddenly not available.
I'm not sure what is best in general for scouting/detecting for military fleets though.
It really depends of what the ship suppose to do to be honest. My scouts have only large EM and TH sensors as they usually unarmed and an Active Sensor will just make them more visible without any reason. However, if is a scout marauder tasked to hunt down commercial ships or to test enemy capabilities then he may have only Active Sensors as he may act with a passive sensor ship as support.
Specifically for detecting ships, is one better for detecting large ships and one better for detecting small ships?
TH Sensors will detect ships of any size in any case while EM sensors will be more effective in detecting Active Sensors so if the ship you are tracking have the Active Sensors on you will be able to spot it otherwise against ships they are useless.
If I was saving space on a small passive scout to go ahead of my fleets, which would you recommend?
As said, it depends. Is the scout for detection purpose only? If yes a big TH sensor is what you need. This will potentially also detect missiles.
Alternatively on a capital ship, for backup detection if there isn't a main sensor ship available, which would you go for?
Cannot really help here, I don't like "blind" capital ships.
Is there a better choice for a carrier to detect passive targets for FACs/Fighters to launch at if not using active scanners?
My carriers rely on small range sensors as they are used for their defenses and recon. However I always have 3 scouts acting as recon group. 1 Carries EM, 1 TH and one Active Sensor. Generally speaking though, I think that multi purpose carriers are not that advantageous as I've found out them to be neither fish nor fowl. I have 2 or 3 design of carriers depending on the mission which can alternatively act together.