The main basis of my incredulity is that even the most uneducated Norse Christian knew what paganism was after centuries of Christianity, so I don't see why a Y90 pagan wouldn't at least know about Christianity and have a vague idea of what its symbols looked like.
Not quite correct. Most Norse Christians of the past
thought they knew what paganism was like though: evil, sinful, wrong, occasionally deserving of death... while continuing its traditions. A Norse Christian would perform some pagan rites without considering the act pagan at all, or themselves a pagan for that matter. Priests of course would firmly disagree.
As for symbols it doesn't take long for a symbol to change its meaning, just look at what happened to the swastika during WW2.
Which would be less of an issue if Christianity just wasn't an issue in the story line. That's my reason for assuming that it won't end up being a big part of the plot. The more Christianity is made a part of the main plot, the more this ignorance cries to be explained—and really, is that the story we want to hear? Is that the story Minna has been building up to?
The first question can only be answered for one's own self, but personally I would very much want to hear that particular story. I find all the religious aspects of SSSS its drawing point and it feels good to see one's own group (in my case Fennopagans) represented in a realistic, serious and well researched manner. As for the latter question... we'll have to wait and see, but my experience with Minna is that she'll always surprise the reader somehow.