Sorry then if I have unwillingly disturbed one of your Posts to come.
I can think of two other means to explain why spies would manage to get behind the lines that easily. If you are a very mean race, you might send these operatives when both your Empires are trading and your relationship is good. You would then check all the entries within the Empire, but as the spies would be already in, it would be much harder. Unless the target is a most paranoiac and isolationist Empire, or unless you are yourself a warmonger that is.
The other way would be to disguise spies as "political refugees" if you do feel like generous. It could even be some famous scientific team looking for leaving the corrupted Empire in which they live, and who were working on some special weapon of tremendous power. You might be tempted to allow these disguised spies to enter your worlds, and then...
Obviously, these ways would never, ever, always work, and that's why I don't quite like the current system "all or nothing" linked with Intelligence. Do you only need to bypass Counter-Intelligence to successfully plant a bomb on a given ship without any chance? Or to kill these hundred million settlers? And then you fail to pass Counter-Intelligence, not only you don't have the slightest chance of succeeding in your project, but you will be immediatly detected and the target will know you were attempting some actions. That can unfortunately led to some infelicitous diplomatical incidents, especially when the target was only looking for a pretense to declare war.
But I seem to digress.