One story I read got them together in a way that makes sense, but goes into some dark territory.
The episode where the Hirogen turned the ship into a killing ground and made the crew think they were other people, unable to remember their real identities, included a Nazi scenario. Seven was a freedom fighter and Chakotay was an American who came to liberate the town.
The story has the premise that Chakotay and Seven's alter-egos had sex, and Seven became pregnant as a result. She did not discover this until some time after that situation had been dealt with and the Hirogen were gone.
To say it was a shock to both of them would be mild, as it was strictly speaking non-consensual (neither of them in their proper, consenting minds). But Chakotay decided that he wanted to give this situation a chance, and so they became close... eventually becoming a family.
The Hirogen had had the ship for a month.
Naomi had been in her room the whole time, which means that some of the crew, some of the time are confined to quarters to cool down rather being constantly played to exhaustion on the holodeck.
On DS9 Sisko and Cassiday went to the Doctor once a month for a contraceptive shot. As long as one of them had an active dose inside them they were both safe. The Doctor on Voyager would have been on top of that, especially if no one was in their right minds and not using temporally appropriate contraceptives for 15th century Klingons or 20th century yanks abroad.
"I guess" that the Hirogen got bored easy and phased out simulations after 3 or 4 days, since we saw them about to move on to The Battle of Wolf 357, because they were dog tired of France.
It's conceivable that Chakotay and Seven might have hooked up, even though her character was a lesbian, but here's who I really think sent half the crew to the maternity ward: Neelix.
Post Battle Orgy.
"Because later that night, Kahless and Lukara jumped on each other like a pair of crazed voles. Grrr."