YES
You will have to re-jet. The bikes come from the factory very rich anyhow and you would need to rejet it even if you left the lid on, as far a the pipe goes, Yes the factory pipe is double walled and VERY restrictive and a new pipe is probably the biggest BANG for your buck as far as a performance mod goes. You basically have 3 good pipes to choose from them being FMF REV, FMF GNARLY, or Pro Circuit. All three are good pipes but all three do different things to the bike. I went with the Pro Circuit only because is creates power gains across the entire powerband from top to bottom.
Good Luck, Obie #8 ;)