I’m trying to work this through from the angle of what we learned in SNW S2E3 Tomorrow and Tomorrow and Tomorrow.
Now that it’s reconfirmed that Star Trek doesn’t have an infinitely ever-branching and expanding multiverse (unlike Marvel or DC), we need to consider how a resilient Prime timeline (river of time) would affect how the fractured timeline in this episode healed - and therefore who would remember what.
In the SNW episode, La’an (and presumably Pelia) are exceptions. Others in the 22nd century aren’t aware that key events like the Eugenics War and Khan’s birth have slipped in time.
So, in Voyager, it seems as though anyone in the crew who did not receive the treatment would not have been able to integrate memories from across the fractured timeline and would only have what they knew in the current one.
As for Janeway, it does raise questions about her foreknowledge. It’s also the case that she would know that the major events related to what they experienced was likely, but it could slip by years, and with sufficiently major interventions the timeline might fork. In fact, the future shown in the episode could have represented a fork that would occur if they did not undo the fracturing.