Sergey Brin in 2013? Not technically a CEO, but comparable.
https://en.wikipedia.org/wiki/Sergey_Brin#Personal_life ("...after Brin had an extramarital affair with a Google Glass colleague")
Steve Jobs had a daughter he tried to pretend wasn't his (the namesake of the Apple "Lisa"),
https://en.wikipedia.org/wiki/Lisa_Brennan-Jobs ("Jobs initially denied paternity for several years, which led to a legal case and various media reports...")