Whoever is calling them Thomkins is wrong. The muzzle weather seals are called tampions, borrowed directly from the the Old German tapon which was greased rag stuffed into a field piece's bore for transport, imported into the Old French tampion and from there into the Royal armed forces and eventually into US Naval jargon.
In WW2, when the Navy warships went around "cocked and locked," when out of home port, they often used waxed canvas muzzle covers cinced up around the barrel, which definitely could be shot through without worry. If you blew them off, the Boatswains just made more. On my destroyer, we still had a pattern for our 5/54s though we never made one.
As someone already noted, small arms are kept in the weapons lockers. When we pintel mounted M2s for duty in the Persian Gulf in the late 80s, we had to fashion weapons covers for them out of heavy duty tarps to cover the weapon and its mount, complete with a steel deflection plate, as no one at SIMA in Subic bothered to scare any up for us.
Our "modern" guided missile destroyer's designers had never envisioned us needing .50 cals and so they were totally field mounted to confront mines and Iranian motorboat attackers.
Every new generation of warships seems to discount the importance of guns to a warship. Odd how they never seem to learn from the lessons of the past that not everything can be readily taken care of by some automated cannon and a passel of missiles.
I do note though that beginning with the USS Winston S. Churchill DDG-81, the Navy has upgraded the effectiveness of the main gun by increasing the caliber and the firing speed, so maybe not all is lost on them.