I didn't answer to your post in particular, as I was writing my own answer when you have posted your point. It gets somewhat complicated.
Contacting a captain can be done, or cannot, depending on how you think communications is handled within the game. And likewise, you may consider there are a lot of ships going in and out, or merely a few, making travel much easier or harder. So on this peculiar area, your mileage may vary.
However, it does raise a problem when dealing with Psychic races, Hive races or something along these lines. That I will leave to the attention of someone roleplaying one such race.
I admit the fact that a few spies can make it behind your lines doesn't bother me too much, but I gather we have quite different conceptions of how a stellar society would be built, and so it would be much easier to be a spy in my own Empires than in yours. Or perhaps I am not yet cautious enough...
What does annoy me is that you will *always* know who performed an Intelligence action against you when it fails. Is Counter-Intelligence so efficient all spies are caught red-handed alive? (It might be hard to know who was trying to assassinate your ruler if the ship ferrying this spy was blown out "just in case" by planetary defences) I am also wondering if you could recruit spies from another race to confuse things all the more. If you happen to play the EEE, your spies might be quite easily identified.