My initial response to this ask is that Bonnie is probably not at the technological level to recognize something from Azgard level tech (that’s what the Infinity Stones are, right?).
And then I realize the whole Thanos thing didn’t come out of the blue, it started with relatively minor things like Iron Man’s appearance on the world stage, going into the first Avengers movie, the Shield Helicarrier thing in Winter Soldier, and then the Ultron event. Which means the crew would have had plenty of time and opportunity to become aware of the escalation going on outside their immediate vicinity.
In this time, it’s highly likely Box would have scouted out and brought back some of the alien tech among the debris and everyone would have advanced technologically as a result. So Bonnie (and/or maybe Chica) probably would have had the calibration to sense the Infinity stones and the Snap, just as likely as Freddy would have hacked into and stolen a lot of secret Shield and Stark (with a small chance of Wakandan) schematics, and Foxy now being secretly powered by an Arc reactor.
All of this done on a just-in-case scenario, of course, as Freddy is cautious like that and likes to have his options open in case of disaster. It’s unlikely they’ll reveal themselves without being directly threatened, especially with heroes who appear to be actually capable of handling the threats as they come, and with them busy with their own task.
But then again, after Thanos dusting half the world’s population of children, they may come to remember that one dreadful night in ‘87. It’s... interesting to realize that Thanos can be described, perfectly, as a Purple Guy.
