No, they don't have the same meaning.
'Are you into that?' means 'Are you interested in that?', with regard to a particular subject or activity. We use this to talk about people's hobbies and interests.
'Are you after that?' is not a common phrase, and it can't - as far as I know - be used to mean the same as 'Are you into that?'.
Colloquially, if you say that you are 'after' something, this can mean that you are looking for something. For example, if someone comes into a room and starts looking through all the cupboards and drawers, another person could say 'What are you after?'. So, 'Are you after that?' could possibly mean 'Are you looking for that?'.