When you go to a park, often, you'll see cannons that have been plugged. But you can still see that they were cannons.
I think welding over the openings really ruins the look and historical accuracy of this sub. They should have put a round plug in if they just needed to block the tubes.
If they were trying to make leaking tubes water tight to make the sub sea worthy, then I could understand welding patches over them like this, but this sub isn't in the water. It's on land.