You have to be careful what animation .an files and .ani files are applied to models...just because some models contain the same name, they may not contain the same bone elements and that will mess up the animations if they are not meant to correspond. Of course a safe way is to copy both the model and animation .an file (the binary file used is listed at the top of the .ani text file), and the .ani file, but that might also screw up the look of the model if the character's textures are not also copied...again, the same applies that textures with the same name between games are not always really the same file because someone may have edited them.
As for lanterns, you are correct that the POTC/NH ship models probably don't have the light/lantern locators defined in the model because that feature did not exist in the earlier Storm 2.0; this source is derived from Storm 2.8. Even if some ship models were copied that do have the locators, there is also some script code that would need to be added to turn them on/off when the time of day changes to night/day.