I see your point. But if you look again at the three inch gun on the seal and note the positions of the hatches forward and to the left and right of the gun.
Here are a few picks of the Squalus while under construction in 1938.
Note that the foward gun mount is there (that flatheaded mushroomy thing). Also note that under the surface of the platform the support for the mount are actually smaller than what sits flush with the deck. Now refering back to the seal picture and the location of the boat hatches.....
Here is the aft section of the Squalus showing that she was indeed constructed with two deckgun mounts in 1938 when she was being built.
So both platforms for the guns are there and the supports to the platforms are less intrusive underneath the deck which, for me at least, still points to the boats were pulled and replaced with external tubes.
Going back to the Seals ovehaul picture the gun is positioned right at the end and inbetween the boat hatches.
If they didnt use the hatches then the only other place to put them would be to lash them down above the deck.