Hmm, that sounds complicated.  Im not that great at this, all I did to make the ship styles was follow Kryo's instructions on making custom ship styles.  I have no experience modding or anything like that.

How would I edit the hardpoints so they are inside the hull?

I noticed the star trek mod made their components invisible, thats why I asked but if its easier to make all of the hardpoints be inside the hull, then I just need to know how...

Thanks

Alternately, there is actually a mod already that does this (UDFM), but it hasn't been updated recently. To get the same effect, if you have KHSM you can just replace all of the weapon model files with the blank model. Lots of manual work, but not difficult by any means.