Spear,
There is some debate about the 4 enlarged stanchions on either side of the fairwater. Without a doubt, they are gunmounts, but the "patrol record" that that museum sells in the gift shop (it is basically excerpts from the boat's smooth log and other misc. info) lists them as mounts for .30 cals. I'm not sure I believe that, and so yes, I'd say they were .50 cals. Were they carried aboard or not? Tough to say. If you'll notice on the patrol record, the sub destroyed 14 mines. At LEAST one of them is listed in the record as being destroyed by gunfire from the boat when they were surfaced, and I would assume probably with one of the machine guns. The armories aboard subs were said to have some springfields or M-1s, some 1911's but I'm not sure you could destroy a floating mine with something that small.
Would the patrol record have been painted on the fairwater during service? No. In fact, even when she changed designation to an AGSS, I don't think it was painted on there. However, there is some talk of "brag rags" which were small Japanese flags that might be flown when coming into port after a deployment to indicate ships sunk. Aside from that, there's always the "clean sweep" broom, but again, I'm not sure how often that would have been flown. To my knowledge, these days brooms are typically only flown aboard after a shakedown with the manufacturer.