Ron Moore even claimed in a DVD commentary this is how it's done in the US Navy
He would have been correct until the 1990s. But US Marines were gradually withdrawn from USN shipboard security assignments after WWII, lingering the longest aboard ships that carried strategic weapons. The deployment of tactical or strategic nukes on surface ships has been drastically scaled back now, and while there no doubt are live warheads available to select vessels at select times, the training of the manpower to have them there has been scaled back, too, so probably very few ships actually carry such "secret" weapons nowadays.
Supposedly, nukes were rare strategic assets aboard the nuBSG battlestars, too, so perhaps Marine guard was warranted as standard for that reason? Perhaps lesser vessels, or battlestars armed with conventional weapons, would have been guarded by units without special status and/or less in the way of special training?