With regard to the torpedoes themselves - I think the dialog stated that the fuel compartment had been altered to house the cryotubes. So I'm guessing they had live warheads (perhaps that is something that can be easily deteteced by scan) but if you tried to actually shoot them, they wouldn't go anywhere.
Marcus knew about Khan's people being in them, however, and he still expected Kirk to shoot them at Kronos. If they don't go anywhere there's no incident. Unlikely as it may seem, the torpedoes are just designed to work normally even with the introduction of the cryotubes.