I guess the answer is no.
"I'm not sure you can go by the paint scheme"
I am.
"You should check the level of the bottom and the screws"
I did.
"Often rough seas will lift a ship over a torpedo"
Almost a flat calm.
"Also, it could be a mod issue"
GFO and Gone Asiatic, neither of which mess with the draft.
You often see this on the 10,000 ton tanker, if it's loaded the freeboard is almost gone, if it's in ballast (empty) there's several feet of red lead showing below the plimsoll line. Never saw it with a warship before.
That's another shot of the Shokaku in better light;
That's a different one with the correct draft in Manila Bay. Some kind of glitch with that task force, north west coast of Luzon in March 42, affects only the two SHOKAKU carriers. The MOGAMI and MAYA heavy cruisers and the battlewagon all have the correct draft.