The first 6 months of their relationship, she was a kazon slavegirl who probably at the least had he ass grabbed 5 times an hour like any waitress in the real world too... Do you really think Neelix, half a sector away, was celibate while whatever was happening to Kes was happening to Kes in the Kaozn camp?
Bad shit happened after dark.
Besides there's this thing guys do where they have secret sex with other women who they are not married to while they are married... I think it's happened at least twice in the history of the world. If Neelix was screwing around on Kes, it would really explain his ridiculous jealous streak that his own unfaithfulness would explain his lack of faith in her.
Seska was frakking Jonas?
Seska was frakking Jonas.
She got power and leverage from secrets.
If Tuvok knew that Jonas had been frakking Seska, then finding the mole on Voyager wouldn't have been that difficult... Or the Vulcan was having trouble tracking her 9 to 15 "known" sexual partners, including Chuckles.