The FAQ refers to various sources where SCS Representatives, namely Jamie Carlson, have explicitly given their Ok to change some things. Here is again a link to one hard source where SCS (by way of Jamie) gave his Ok to certain modding efforts
http://www.simhq.com/_naval/naval_019d.html
As you can see, more or less
everything short of new/added playable platforms is Ok! To make it more clear, changes in the DB, new textures and models, new sounds and so on is alright. Only when you add a new playable platform regardless of how you do it are you stepping out of bounds. The only thing that is unclear (but I think SCS is Ok with it) is adding a different type of an already existing platform. For example an 688 Flight I or an Indian Kilo.