A bit of google-fu shoved me this: native bullet definitely does support convex hull collisions as btConvexHullShape and it should give much better result compared to triangle mesh collision, even on simplified meshes.
Question is if it's implemented in JBullet and how many compound convex hulls you'll need for complex geometry.
Regarding optimization - it's completely possible to generate convex hulls in runtime, enclosing multiple blocks if they fit convex hull limitations. And you're completely free to change collision level of details for blocks - for example, fully enclosed blocks could be simplified to boxes and merged by simple optimization algorithms, while exterior blocks could be subjected to different collision detalisation levels based on overall ship size.
And, by the way, it was you, who said that most modules are boxes anyway - it means that there will be not that many blocks to use convex hull collisions for.
Another thing to note - with good convex hull building algorithms you could use blocks like slopes with no additional cost, and believe me, they look much better than plain boxes. I'm telling so not only from block-building experience in games like Space Engineers, but, coincidentally, I'm currently developing a game with block-building elements using UnrealEngine4 and went through all the way from plain boxes in grid, through various models in grid and, finally, to free placement (still have to find good balance between batching, greedy procedural generation and instancing at this moment).
Just in case if you ask what UE4 user is doing here on JME3 forums - I have JME3 project as well. Kind of - it's suspended until I have better financial support. Ironically, survival-shooter-sandbox built in UE4 requires much less financial investments than "simple" board game, combining ideas from MTG, chess, civilization and lots of other sources (mostly - unique art and models for characters plus matchmaking servers setup and upkeep costs, and it requires more advertisements too).
BTW, did you try to experiment with Bullet constants like minimal object size? In your world built from blocks it could greatly improve performance (or completely destroy it).