Depending on the context it can mean either why or yes.
Example 1: Use of y as meaning yes
d00d1: is the train supposed to leave at 6:30?
Example 2: Use of y? meaning why?
d00d1: u wanna come see the new teletubbie
movie with us?
d00d1: its super cool!
d00d2: stfu fag
***d00d1 was blocked