The pace in online games is too fast (4s per move usually, with a 12m buffer) to use pen and paper aides. Short of having some sort of screen-scrabbing AI-tool that auto-labels pieces as they are revealed (doable by a decent programmer, but Stratego is no poker, there's no money in it), I think it's safe to assume top-level players don't cheat. Top-level play in live tournaments has a high correlation with top-level online play as well.

Seems like it would be easy to test. See how the AI does when revealed pieces stay revealed compared to a standard game.

It would effectively need to be a different AI to use that information. And what does it play? Humans? Other AI?

Also, given this is online competitive play likely that a significant portion of top human players are cheating and have aides to keep track of pieces.

That's a great point. It may even be condoned in some circles.