I was about to edit a script to see why my slave wasn't meeting the requirements for a quest, only to find out the scripts are compiled now. :(
Or does Godot 3 do this by default?

Yes, godot 3 binarifies them by default. I might try to reverse it in some time. 

+1 for this request. I like to poke around in the code to understand the game better, but no luck with the current build...