Accordion mystery hose?
 

http://www.4cefed.com/forsale/techno/accordianhose.jpg
^^
Where does the small bottom hose connector plug into?

Power steering idle up. A vacuum hose goes from there to a tube in front of the power steering pump.

What negative effects would this cause if its disconnected? Cause mine has never been conncted.

Your idle will fluctuate, maybe stall, while you turn the wheels while idling

NO. That hose connection on the accordian hose is so the air going into the power steering idle-up valve is 'clean'. If the hose is not hooked up, unfiltered air will be sucked into the accordian hose, AND into the P/S idleup valve (and on into the throttlebody). dirt=bad