Cold air intake replaces the old intake system, but I thought the throttle body replaces the intake system also so can you have both?
Two completely different components. A cold air intake simply relocates where air is gathered from, the TB controls and measures the amount of air allowed into the engine. It also typically houses the throttle position sensor (TPS)
Your ITBs will have separate intakes for each cylinder therefor you would not be able to use a cold air intake system.
ITB's means individual throttle bodies meaning each intake port would have its own throttle body. if you have a single throttle body then you do not have ITB's. ITB's dont normally have air intakes above the trumpet inlets for the throttle bodies as the velocity is generally affected through the intake trumpets. You can remove the trumpets and add a common plenum cap and then go to a single larger intake plenum to an intake pipe and then filter but I wouldnt really attempt to do air filters unless space is not an issue. there's a reason all the old hotrods simply used tennis balls over the intake trumpets when the car was off versus putting on air filters lol. even the honda boys that go n/a and ITB dont normally have air filters.