A lot of stuff is affected already, more than I tested in fact; a lot of zones are shared by ships. For example, nearly every class classified as "freighter" in the game shares the same engineroom. When I make a change to that, it affects them all.
Compiled a spreadsheet listing all the zones used by individual classes:
http://www.filefront.com/15845937/SH5_FlotZones.ods/
Maybe someone has use for it. Sorry about using FF, forgot my Rapidshare login.
* I changed NFlotMain and NCargoFuel. So as you can see, most ships you run into on a regular basis have been altered already. Just need to do a lot of testing to fine-tune (hence the request on feedback).