When you say it's running a "bit hot", is that as indicated by the CPU temperature sensor, or by feeling the heat output with your hand? If it's the former, what temperature is indicated? As these machines are fairly old now, it may be that the thermal paste between CPU and heatsink has dried out and needs renewing.

It's probably also worth cleaning out any dust bunnies that may have taken up residence.

I would assume (not that I know) that your surmise about a single processor running cooler is correct, and it would be true that a faster single CPU is better for OS 9: if you decide to go ahead with a swap, it's probably best to make a listing in the Trading Post. NB; the fastest CPUs (like the 2GHz part you mentioned) are third party upgrades from the likes of Sonnet, not OEM Apple parts.