It is a little weird for ships given to non-DLC-owners to just be, essentially, templates with gaps in them.
Personally I think the best way would be for mods (via direct downloads or as user content from the Workshop) to have all parts visible. From weapons like Franco said, to actual content packs like Petri mentioned. I don't think they shouldn't show up, I think they should be there for everyone. The DLC parts are awesome, with the cockpits added by Founder and Registration packs being more visually appealing than half the things already in the game.
I believe the all-around best solution would be to have them show up for all players, but people without the DLC can't move, scale or place the parts if they try and edit a ship that uses DLC parts. That way mod authors could make any design they want without that annoying "how do I balance aesthetics with usability" thought.
It would even give players without a DLC a chance to see the parts themselves without browsing for screenshots, and the fact they can see but not personally use DLC parts would give them a HUGE incentive to buy.
More sales for Stardock, more freedom for modders, more attention for Workshop creators, more ships for everyone.
I'm not going to pretend they're going to update how DLC parts are shown, and I'll try to say the least bitterly I can that they're probably too busy with a new paid DLC in the works anyway, but it would be nice. However I adore the game, and I should just be thankful that I can make 3D spaceships and fictional races in a matter of minutes thanks to Stardock's hard work.