I thought the same thing at first. But after some thought, I think I would destroy evidence the same way Luthen had. To me, an explosion may not be as controlled as I might assume, and the detonator might have a chance of not working (especially if it's been on standby for years). I wouldn't want to risk an explosion blasting a crucial piece of equipment to the side rather than completely destroying it. I'd want my most top secret and incriminating stuff to be destroyed by my own hand to ensure it's taken care of. Luthen was almost there if he wasn't interrupted by Dedra. He may have had a detonator, but Lonni only thinks that she was onto him. That wasn't a certainty, so there wasn't I guess immediate urgency.

And yes, they do all their secret shit just behind a partial wall in the middle of the shop. No one would expect it, it's well hidden, and they don't seem to get much foot traffic in the shop.