Although some have reported different experiences, I've always found this to be true with regard to MFM vessels...
If the ship is not flying any flag, the hull markings are "eye candy" and are for you, Herr Kaleun, to determine if the ship is a valid target based on the circumstances of the moment...in that condition, any ship in a convoy is fair game.
But, if the ship is flying a flag, the status as a neutral vessel, or not, is based on the real-world conditions as of the date which you've reached in the game (refer to the pull-down "Schiffsflaggen" booklet, or print it out and keep it handy at your desk).
