Heater hose goes into intake manifold on '86 2.5?

What's this? This jeep is new to me, and I'm replacing all the hoses. One of the heater hoses goes from the thermostat housing into the front of the intake manifold; then it goes out from the back side.
Can I just bypass this?
I know nothing about this engine yet.
Thanks

BTW, can I swap out the throttle body and air box with a 4.0 model (or any other upgraded intake)?