Sorry, there are many ways for water to get into the frame. Just power wash the frame and see how much gets in when you tip it upside down. Anyway the holes are to let the water out and not accumulate and cause rust. This is all well documented in the Hondaman book. Do you have a copy?
I have been a welder most of my life.
I have cut many tubular structures apart and if the tube was sealed and we cut it apart years later there was almost no corrosion.
I have also built tubular aircraft engine mounts and studied the history of those structures too. Sealed tube - no corrosion.
Normally people do not power wash a motorcycle. It can force water into air boxes and electronics.
I would not power wash a motorcycle frame. But if water does get in the frame let it dry out completely and seal up any places that water can enter.
If the motorcycle is stored indoors it usually will not get pounded with water.
I would find out where the water is getting in and seal it. But I would not weld everything closed. as this can lead to other problems structurally(distortion and shrinkage). Heat affected zones from welding must be carefully considered and unnecessary welding can actually weaken the frame over time.