I suspect it was a combination of the B-50 being more capable and hence more valuable for SAC, combined with the numbers of airframes available. Per Wiki there were 3970x B-29s built and only 370x B-50s.
I do not know how many B-29s were still operational during the Korean War, but since the B-29 was good enough as a bomb truck to carpet bomb troop concentrations, villages, and cities from 20,000+ ft there was really no reason to use the B-50s.