You should be able to do this in DA by just making custom ship styles, and naming the themed ships' files appropriately so they only appear as templates for their own styles.

how would you access them from the game without triggering a cheat event

To do it without modding anything at all (The MetaverseData folder has its own copy of the shipstyles folder), you'd need to just add them as templates under the existing styles and remember which style has which ships. Basically a similar method to the meta-safe version of my hull mod.

I'm not sure how the theme mods handle the ships, so some of this may not be necessary and you may be able to just copy the files already included there.

1) Design a 'ship' using the themed hull of your choice. For instance, the Enterprise. It's easiest if you just design these ships under the existing style you plan to use (i.e., Terran, Drengin, Korath, Yor etc). The default game contains twelve styles IIRC so that's how many you'll have to work with in a metaverse game.

2) Save the design as a template (It's a checkbox option in the dialog box that prompts you for the ship's name and description).

3) Go and manually edit the resulting .xml file in My Documents/GC2DarkAvatar/shiptemplates so that it uses one of the 'core' hulls rather than the extra ones added by the mod. For example, you might change  <Component>Constitution_Class</Component> to <Component>MediumHull0</Component>. So long as the .shipcfg file still points at the Consitution-Class model, it will still appear as that. But the game will treat it as a regular medium hull, meaning it will be useable in metaverse games as soon as you research Medium Hulls.

4) Play a metaverse game with the ship style you saved the designs under and enjoy.