It sounds like they're going to get included in the no-weapons rule. The augmentation process knows no bounds, and not even stuff in hammerspace is safe. There will be chances for him to get those weapons back over the course of the game, though!

The exception to this would be if those weapons were literally created out of nothing, and not just stored somewhere--then they might count as a power. If you feel this is more the case, he can keep the ability to create these weapons... they just might not appear if he intended to use them against the ship (or possibly crewmates).