Well that didn't last long. Owner of the Japanese boat saying the US are wrong....
Bullets wouldn't have caused the kind of damage shown unless it was more of the shell kind of calibre either multiple 20-30mm or something bigger like 105. Mines and torpedoes can and do their main damage above the waterline and there are a variety of anti-ship missiles/hybrids.
surely the whole point of a limpet mine attack is you plant the mines undetected below the waterline so nobody can see them
why would you attach them in plain sight of crew members on board ship?
Theoretically something like potentially due to limited access - its possible someone was able to approach the ship i.e. as a dock worker or something but not able to get into the water, etc.