While there's no over-pressure in space, an explosion in contact with the hull
will do significant damage. That said, I think magazine cook-off probably wouldn't be a major issue. There's a basic assumption here that warheads require "conventional explosives" to detonate. I'm gonna go out on limb and say, if you can build a star ship you can probably build a nuclear warhead without resorting to large amounts of volatiles.
The exposed placement of the missiles would seem to bear that out. Of course, I have no idea how the creators of the ship see it, but it makes sense. If the missiles were vulnerable to mission kills, they'd be better protected, even on a converted ship. So, logic suggests anything that can mission kill the missiles stands a good chance of mission killing the ship
That's just me, though.