Some say you should but to be honest, I don´t think so. I´ve had stock carbs with K&N filter for years with no problems. First I had short TORs and this summer long Thunderbikes and no problems with either.
The reason I ask is because it seems that after the filter switch I only hear the exhaust coming from the left side. When I put my hand down behind the exhaust I can feel alot more force behind the left exhaust.