My favorite "spy" unit I've seen in an RTS was way back 30 years ago in Command & conquer: Red Alert.
To you, it looked like a guy in a tuxedo (think: James Bond), but to the enemy it looked like just one of their own soldiers. So, then you could move your Spy into the enemy base relatively undetected. The only detection methods were the fact that you couldn't command an enemy spy to do anything, even though it looked like one of your men. This would clue you into the fact that it was indeed a spy. Also, one faction had Guard Dogs that the Spy had to avoid, else they'd detect him and maul him. The Spy could infiltrate enemy structures and you could then see what that structure was doing. The Spy could also "Sabotage" the structure by damaging it by a certain percentage.