Destiny took a generation to build, its not becuase its small. You also have to remember that the shuttle is about as big as a Al'kesh. There can be atleast two on the ship. But there is three different shuttles pads.
The shuttles are no where near as big as an Al'Kesh, in fact they're not even as big as a cargo ship. Just look at the size of the interior.
Destiny is described as a massive ship.
When/where?
It's Destiny's power conduits that are physically damaged beyond the also damaged self repair systems to fix. So all the naquada in the verse wouldn't help, beyond turning on some lights.
Or weapons, or shields, or the FTL, or pretty much anything else on the ship...