I had this kit as a kid and was a great bathtub and pool ship. I bought one when it was re-released, knowing that it's nowhere near modern standards.
Your gun tub fix looks good; it looks like a field mod (which it is, sort of). Maybe put some bolt or nail heads/holes. You can also add a wheelhouse like the one in the Monogram 1/48 RAG Boat.
Found this build.
The "bathtub flotilla" was a large organization that occupied many household bathtubs back in the day before we all realized that taking a shower was much quicker and the bathtub flotilla faded away except for the memories in later years.
Thanks for finding that link to the LCP(R) Command and Control Craft, that guy did a great job on making an overhead structure to fit his model. He too quickly abandoned the kit parts for the weapons and gun shields and rightly covered over the offending hole in the deck.
As far as adding rivets or in this case very tiny bumps to the surface of the deck per your suggestion. I had not considered that since a lot of that field work would have been ad hoc and in the case of small craft/wooden boat repair there was a layer of canvas laid down to seel the hole from water intrusion and any surface feature standing proud of the deck surface would have been an issue for quicker wear and tear by abrasion. I hope with a good coat of paint that the filled in areas will disappear from casual view. As an interim fix I do have some blanking plates from the Monogram B-29 kit for the Silverplate nuclear bomb carrier version that would have been even more useful for filling the holes. Maybe on the second UDT Boat (I have two of course) that approach can be taken.
***Edit to correct spelling error -- jjf