As far as I'm aware they do. I bought a used Kooba Sienna from their outlet and it was real.
The only thing I'll say about buying their used bags though, is that you need to be careful. The Sienna I bought was in horrendous condition when it arrived. It wasn't stuffed so it had been smashed into the box, so it was misshapen. It wasn't in it's dustbag. The outside was scratched and beat up, and the ends of the straps were curling upward. Also, the braided tassle ties at either end were frayed, and one of the knots was completely undone.
When I returned the bag per their instructions, it took me WEEKS to get my refund, even though they received the bag back within about 5 days. (I returned it the day after I got it.) When I called them after the first couple weeks to check the status, they informed me that only one person deals with all of the outlet items! So they are slow as molasses.
Personally, I wouldn't buy any leather bags from them. People obviously treat the bags they get from them like crap because they didn't shell out thousands of dollars for them, so they're in awful condition. Maybe fabric bags that wouldn't show wear as easily would be fine purchases, but I wouldn't trust anything else.