That entirely depends on how they work though. If there are counters or interactions where you can protect yourself. Capture enemy agents or even lure them into thinking they succeeded (that shield generator isn't down at all) then it becomes a give-and-take kind of game.
If it's simply a matter of "invest amount X of currency Y and wait time T for enemy resource Z to blow up" then not so much.
That's fair, but I think I would have two concerns.
First, I think one of the core problems is that it's far easier to make espionage systems sound fun in our heads than to actually play that way. For example that description sounds like a great movie, but how would it work in gameplay without RNG? Or without the "spend X, wait Y, get Z" mechanic? If they launch a mission to disable a starbase, do I have a counter-mission that always makes theirs fail? If so, why would anyone bother at all? Or if my mission has a %-chance of making theirs fail, we're right back to trolling territory.
Second, while espionage games can be fun (see Invisible, Inc.), they're simply a different type of game. Even if we could build a system like you're describing, or the micro-intensive spy ship system described in another post, it would feel like adding dice to chess or deckbuilding to Starcraft. Not bad mechanics in and of themselves, but they can be disruptive if they don't fit the existing gameplay.
I feel like Stellaris sometimes has that "last game you'll ever play" vibe among its audience, that it's supposed to be all-things to all-people. In my opinion one of the biggest reasons why its design continues to struggle so much is that the devs embrace that to an unhealthy degree. I would argue that a detailed, spy-vs.-spy system falls into that category.
Carefully navigating agents through a space opera
does sound like a great game. I hope someone makes it. But it sounds like an entirely different game, and personally I think it would be frustrating to basically have to play two games at once. That's doubly true since espionage systems tend to be either over-powered or under-powered. If you can cripple someone's starbases or entire fleets, then it would be incredibly frustrating to have someone win just because they were better at the espionage minigame. If you can disable a single ship or blow up a building, then it's another ignorable mechanic.