You didn't specify year / model etc. My IAC valve has one coolant hose
going to it (the return is directly to the manifold, no hose). I can't
imagine what harm can be done by disconnecting the hoses. The only thing
to be cautious about is air pockets in the cooling system, on some
Hondas it can be tricky to bleed the cooling system so it is free from
air pockets. When the car heats up, are the hoses to the IAC valve hot?
If so, you should be fine.

Then again, not knowing what car you have, the above could be utterly
irrelevant to you.