Although citizens of Canada who are traveling to the US with a Canadian passport do not need an ESTA, does Cuba’s designation as a state sponsor of terrorism result in any limitations on Canadian citizen eligibility to enter the US after having visited Cuba?
No. Canadian citizens don't need ESTA because they are not using the visa waiver program. The visa exemption applying to Canadian citizens is enacted separately (by regulation at 8 CFR 212.1(a)), so the statutory restrictions applying to the visa waiver program (8 USC 1187(a)(12)) do not affect it.
I recall having seen an official page from CBP or perhaps the Department of State saying as much at some point, but I can't find it just now. The closest I can come is a page from the US diplomatic mission to Canada describing the circumstances under which Canadian citizens need a US visa. The only text that would apply to a B-class visitor visa does not mention Cuba (or the other countries that are significant to the VWP):
Furthermore, Canadians who have been removed from the United States or who have a criminal record, including for driving under the influence, will need to follow a separate set of procedures to enter the country.
But this links to information about getting a waiver of inadmissibility; its not as simple as triggering a requirement to have a visa.