The missiles were found rather early, before the regime fell, one of the first targets in the uprising was the armories.
If you were going to stage an uprising wouldn’t the armories be your first target as well?
As of March 2011 with Tripoli still holding out the rebels held twelve big armories and the ones holding them are openly hostile to the US but warm to Turkey :
http://www.theguardian.com/world/2011/mar/01/libya-rebels-weapons-store