Why does One Piece antagonist disappear after being defeated?
In most of the cases, the big villains we've seen have been arrested by the Marines after they were defeated, so they would not get such an opportunity. We see most of them in the Impel Down arc, locked up.

Specifically, in the case of Arlong that you mentioned:


   It is currently unknown where Arlong is being held, since we didn't see him 
 in Impel Down, but he is being held by the Marines somewhere.