Satellite telephones are one way the ships could communicate. Depending on how far apart they travel, they may have some short range directional antennae, or they may be operating on a schedule of some kind, putting into port at regular intervals and communicating via messengers. There is very little that they would need to communicate that couldn't be passed in everyday, but coded, conversation.
As far as them scuttling the ships, they may already be wired to explode with the push of a button. Without knowing how the crew would intend on scuttling it, any commando raid could very easily find themselves landing on a sinking ship.
Of course they can always just listen for their "go code", whatever that might be. Just hope it wasn't something OBL said on the latest tapes. They might aknowlege the "go order" with very short and seemingly innoccuos transmissions. Very short as in a second or less at a prearranged time and date. Ships could communicate one to another by blinker or flags if they were withing line of site of each other, which I find unlikely.