Is there anyway at all to alter/change the hardpoints on a vessel? ???  I aready know that just adding it in the ship's xml script doesn't do it...

Yep, its actually pretty easy, provided that you don't want them to be targetable. To add a weapon:

 

Copy a Corvette weapon.

Rename

Change the bone's to one that makes since for a capital ship

Change the particle if desired

Then add the new name to the ships hardpoint list.

Your new ship will start using the weapon and it will look pretty realist.

So if I want to add a fighter bay to a vessel, just copy one from a ship of the same class and affix it to the hagarless ship with the change to the ship name that's attached to each hardpoint string?

but if the hard point is not targetable the ship is invinserble

I have yet to run into the not targetable ship invisible problem, and I have added a lot of weapons.

Maybe I should be more specific.  I'm looking to make the Venator capable of launching V-Wings.  I thought adding the launch bay might help.  The V-wing "spawn" code is in there, but none launch.

I've tried that and for me it crashed the game. If you get that to work send me your work!  And ships with an intact hardpoint are not invincible. The ship as a whole can still be targeted, you don't have to destroy all the hardpoints to destroy the ship. However, the AI typically auto-target the hardpoints.