EU4 spans roughly 400 years, and dealing with prisoners and/or wounded soldiers changed a lot during this timeframe.
For the first 200-300 years taking prisoners was highly uncommon in Europe. The usual fate of wounded soldiers was to die of their wounds. Worse even, the usual fate of prisoners was to be executed, unless they were high ranked nobles.
This was different of course in other parts of the world, capturing enemies and selling them into slavery was an important economic factor in many regions, and the practice of "adopting" former enemies that some native americans cultures practised is interesting too, but modelling this is not exactly easy..