The FX update mod will cause ship sinking mechanics to work correctly only if the zones of the ship use the entries defined in FX Update's zones.cfg file. If new ships are made and are setup to use the stock zones.cfg file entries then they will have the stock SH5 sinking mechanics (boring and dull). I went and changed all the stock SH5 ships to use FX Update's zones.cfg file entries in the FX Update mod.
I would suspect that new ships are using the stock SH5 zones.cfg file entries and that is why you see them not listing or sinking