So, you want your NPC's (or at least some of them) to be fully fledged thinking individuals. But you want them to not decide they're in a simulation no matter how much the players try to convince them.
One option is to make them think like normal humans.
Then add some elements to their world. Add an evil empire to their history with a central belief that involves the world being a simulation. Make them really despicable, nazi-level villians who pretty much all the NPC's hate pretty much automatically. Make it so that in the worlds history the way the evil empire justified it's atrocities all revolved around this idea that the world wasn't real and was a simulation to the point that anyone talking about things that sound like arguments that the world is simulated sound very similar to famous speeches from VR-world-history-hitler.
Make their mythology involve keywords that match the sorts of things people would say while trying to convince someone they're in a simulation.
Then add in some non-sentient bots who's job is to act as the random street-corner whackos. They occasionally wander the city streets ingame spouting clearly insane stuff mixed in with claims that the world isn't real and "we're all the dreams of lumps of metal"
"the Administrators (Illuminati substitute) control everything!"
So that almost any right-thinking sane NPC within the game world considers it pretty much a point of honor and morality to outright reject the concept of simulation.
So a player makes some NPC friends ingame and while sitting round in a tavern decides to try to convince their NPC mates that the world is a lie.... so they start to talk about simulations and computers... and all the NPC's within earshot start to get disgusted looks on their faces because to them it's roughly equivalent to starting to spout nazi propaganda mixed with Illuminati/chem-trail/truther maddness.
The inkeeper insists they shut up or leave and their NPC former friends mostly start avoiding them.
Bonus points if a player tries to elaborate "look, I know you think there was a big genocide by the evil empire but it never actually happened! it was all a myth to stop you believing in simulation"
Through all this the NPC's maintain free will.
It's not perfect, some NPC's might get convinced... but the beauty is that they'll just be seen as evil crackpots too.