The rulebook says about mines “and a submarine cannot move into a space with its own mine”
It says about silence that a ship can move “without crossing an island or his own route.”
My guess would be that passing through your mine is violating the intent of the rules. However, a pedantic reading of the wording of the rules (I'm a lot of fun at parties) could be interpreted to indicate that it's allowed. If you're using silence, you're not quite moving into the space, as much as you're briefly passing through it.
It seems the mine rule would control. "and a submarine cannot move into a space with its own mine."
Isn't that the end of it?