OK sure, they do. But on every warship I've ever been on (granted, none of them were Russian), every single person was a trained firefighter and very well aware that there was no fire brigade to call. In particular, setting fire to an ammunition store (as opposed to something more innocent but still vital like the galley) seems like an especially stupid thing to do. I'd also like to point out that every single missile system I've ever seen is not reloaded in any meaningful way at sea. Ships just pull into port an a crane lifts the replacement canisters into place.
Given the potential causes basically being [accident, self-inflicted sabotage, hit by missile], "hit by missile" seems by far the most likely given all the other information about this.
On the warships I've been on, there were only a few well trained fire fighters, and the rest were poorly trained on the job. I doubt if I would have been a very useful member of the damage control team had something happened.
Galley fires could happen anytime. During times of war, guns are being loaded, missile systems are turned on and tested to ensure they are ready. Somebody could easily screw up and cause a major fire. If missiles were fired by the Moskva, then a dud could have caused a fire, and so on.
I'm not claiming this is likely in this case, but it does happen.
Why not consider the sabotage option? A well controlled scuttle will ensure 100% survival for the perpetrators, sure beats dying of Vlady Putin's cancerous convulsions, plus you get to not commit war crimes... What's not to like?
Given the potential causes basically being [accident, self-inflicted sabotage, hit by missile], "hit by missile" seems by far the most likely given all the other information about this.