Actually in Star Fury, which is based on Space Empires, there are quite a few civilian ships going here and there between systems. You might expect a spy to be hiding in one of these freighters as a crew member for example. And even my most isolationist Empire cannot stay outside of trade.
But I admit I have never been too keen on intelligence, although I am not sure why. Perhaps it is merely because I prefer to do other tasks such as spying myself with my ships rather than relying on an abstract project, or because Intelligence is a too risky business, especially when the target knows you have been trying to send a few operatives. Of course, if you can convince a few neighbours to gang on the same target, it is a whole different story.