The COB is the Submarine equivalent to a Command Master Chief. Like any other small command, a submarine may not have a Master Chief assigned to the crew. Even if there is one, he may not be the COB.
Normally nukes do not get assigned as COB because their training is too specialized and valuable for this job. There is a similar position for the senior enlisted nuke on a sub. He is known as the Engineer's Enlisted Assistant. Heis the senior member of the Engineering Department, and functions somewhat like a COB, although the COB's authority and responsibility extends to the Engineering Department the same as the other departments.
By "who holds the keys?" I assume you are referring to those used to launch a weapon. There are several sets of keys that are "official". The Officer of the Deck and Engineering Officer of the Watch each have a set of keys for things like the SCRAM breakers, small arms locker, etc. The keys needed to launch weapons are held by the Captain and Weapons Officer. These keys may or may not be assigned to other officers. There may or may not be additional keys needed to launch a weapon. The entire sequence from receiving the order to launch a weapon to the actual release of the weapon required a strict procedure which includes cypher locks, combinations, code keys, and actual keys. This system is classified. No one without the clearance and need to know ever knows exactly who is holding what pieces to this puzzle at any one time.
