As far as I am concerned about this matter, Napoleon and a few around him knew about the Prussians, but the information did not flow downstream. Talk about conspiracies - one would need to get Royalists, Republicans, and Bonapartists to all conspire to create a fake paper trail to suggest Napoleon didn't know - and why would they bother?
The fact Officers of VI Corps etc. were surprised does not mean Napoleon was. Also note that some regiments of VI Corps had royalist suspicions, and thus Lobau also had reason to throw them into the fight without explanation.
After the campaign is over, I'll gladly take the baton to debate this in detail and have, as usual, a meticulously gathered and large body of evidence that demonstrates that Napoleon was well aware of Prussian activity on his right. He was absolutely surprised by the magnitude, and admitted as much in exile.
The Prussians were tenacious during the campaign, and I certainly give them the greatest amount of credit for the victory. It was they who stymied Napoleon's original plan, albeit with help from traitors - but they still hustled to get an Army into place. Once again they were helped by treason to avoid destruction, but even after a severe pounding reorganized and pushed those same elements to Waterloo where they proved decisive.
They also intercepted (or received from traitors) Napoleon's recall orders of June 17th.