Holes in the hull at sea are not a good idea. But in the superstructure are not so bad.
Re: the Ventura, the article does say the length, but this would be unusual. Author may be confused? It is possible though.
The closer you get to the waterline, the less the liklihood of cracks as the ships movement is less the further down you go.
As to welding..on QE2 we did not have the staff that could weld aluminium plus it would be almost impossible to do it at sea. There was one recurring crack on sports deck they must have repaired 6-10 times. When it came back we would put "Denso" tape on it, paint the tape white, and we would be good to go until the next dry dock.
Possibly more expansion joints would have helped but, they produced their own headaches. Waterproofing, deck movement etc.
Another thing to remember is QE2 was aluminium from q deck up, most of the new ships are steel I believe.