I've just released my Ultimate Design Freedom Mod, a mod that takes all components and makes blank copies of them. These blank copies have all of the functionality of the old, including attack animations or special abilities, without appearing on the ship design at all. The blank components also have a single hardpoint facing the same direction as the original on them, so you can stack components as much as you want.
With the use of Kryo's Hull System Mod, Socially Hazardous's Weapons Mod, and Kaesar's Non-Functioning Engine Parts, you can use any ship-related graphic in the game as jewelry and design your own ship from scratch--then, when the design looks good, you can add modules without any worries at all.
There are only three components that do not have blank copies, as the game will not give them functionality (working on finding a way to fix that): Colony, Troop, and Advanced Troop modules.
What's more, the AI uses the blank components as well! As far as I've seen, it's actually an exclusive thing--since I've installed the mod, I haven't seen a single actual weapon on an AI ship, only blanks, and the same goes for other components. This will clean up AI's designs.
And, of course, you now have the capability to put any model (be it based off of a TV show, a movie, or just your creativity) into the game, and keep it just as it's supposed to look without changing it for your functional components. If you click on the logo of the attached link, the full-size image features the NX-01 from Star Trek, unchanged but fully capable.
And, the blank models have been given their own tabs so as to make browsing easier.
The readme covers how to install the mod alone or with other mods, and I am glad to help if you're having trouble. Post here or e-mail me at email@example.com with questions/comments/concerns.
Update: July 1st (V1.1):
Now includes thumbnails for all blank components, making it easier to differentiate between components and making design maintenance easier.
Features being worked on:
+ Colony and Troop Transport cababilities (Kind of drawing a blank here, go ahead and bump the "Hard-Coded Personnel Transport Graphics?" thread, as there was a dev trying to help me out)