Another way a spy can get into your land is through an open border agreement with another civ. For example, You may control an entire land mass with Egypt, but Japan can slip a spy onto your land by going onto Egypt first (with an open border agreement), then walking accross land to get to you.
If you're powerful enough you can declare war and sink all the subs you see. That would do it, otherwise the normal spy defenses apply of putting units on valuable resources, have the workers to rebuild, and of course hope they don't want to risk retribution and not sabotage at all.
I suppose another way to control sabotage is to improve your relations with the civ in question so they don't want to "attack" you with sabotage.
In this game the opponent is either a friend or an enemy, and your defenses are either improving relations or declaring war.
