Sony is reported to have said that Trophies patched into old games will not be awarded retrospectively.
The decision to not award Trophies in this way is due to the relative ease of save game sharing on PlayStation 3, according to this.
Had Trophies been retrospective, save game files with everything unlocked could have been easily traded, making it easy for people to cheat the system.
This means that should Naughty Dog patch Uncharted: Drake's Fortune with Trophies, you'll need to go through the game all over again in order to get the points up for grabs from it.