Yeah, use a takyubbin service to send your baggage from your Tokyo hotel to your Kyoto hotel, carrying just a small overnight bag for Hakone.

Ditto from Kyoto to your hotel at Itami airport (or if you are actually going to sleep in the airport, send them directly to the airport for pickup).

Will save you a HUGE amount of grumbling and luggage carting up and down stairs and probably only set you back about Y3500 for each two suitcases each time you do it. Any decent (i.e., not totally rockbottom) hotel can handle this if you ask them, otherwise if you have to do it yourself, it is a bit harder but still readily feasible.

If you save putting having to put your bags in coin lockers even a few times that will cover much of the cost.