They have two shuttles, IIRC:I thought they only had one working shuttle left. I didn't realize that there was a native American, (well, native Canuck) on board the "other" Destiny.
1. When they arrived on Destiny, they had two, one with busted airlock.
2. Busted airlock one was left on the planet with the monolith with the people wanting to stay.
3. Other one was destroyed crashing into a mountainside exploring a planet
4. Busted airlock one was replaced by a "new" one when the people from the monolith planet showed up again.
5. They gained another one from the "other" Destiny a few episodes back with the 12 hour time loop.
So they have two shuttles, probably both in good condition.