Why does Charles zi Britannia say "Yes, you're worthy of being called my child now!" at Lelouch's action?
The exploding ship was episode 13, but the Charles scene you're referring to is episode 22 with Euphy.
Charles didn't actually say that, it's a mistranslation. Charles said "he did it, he really did it", and what Charles most likely was talking about was Lelouch developing his geass to a higher level, and not the consequences of that development.