I was on Diesel Boats from 63 to late 74. No 40s, they weren't portable and would have presented too much water resistance. The resistance would have defeated the whole purpose of the Guppy program.
Maybe a 20mm, but they require a fixed mount, and I don't remember seeing such a mount on a Guppy, or among the pictures on Navsource.
50 Cals are possible, but also needs a solidly mounted post. All the Boats, I knew, had portable lifeline stanchions. They're no good for a 50 mount.
The Boats I was on had a couple of Thompsons, <>20 M-1s and 10 or 12 45s. A couple of M-60 would have been nice, but none of my boats had them.
All the Diesel Boat skippers I knew hated to be on the surface, within 5 or 10 miles of a hostile shore. For specops, they used, either, a lock-in / lock-out procedure (close to shore, quick in and out ops) or dive-and-tow for LRPG ops. No surface, no need for deck guns, let the Riverine boys handle searches.
I have a Sub Vets meeting this weekend, I'll ask around.
Mike K.