Tips for Using Spies in Mid-to-Late Game
You need to get your +espionage bonus up and those missions will have decent success rates.
Remember ambassadors and the empire leader can get espionage skills as well.
Best strategy is to find a pirate base and send all your ambassadors who aren’t really needed elsewhere there.
Then have your spies start low-risk missions against those pirates.
To get a leader with +espionage, you just need to dismiss your current one a month or two before the espionage missions end (dismissing leaders is BAD under some governments). You’ll either get a leader with less than 4 skills and they’ll pick up espionage, or you’ll have a chance to get a leader with it whenever a mission completes.