BigEd, I think you are missing the point: any computation a 6502 can do, a simulated 6502 can do identically.
While the general answer is 'no', there are situations where 'fingerprinting' of some sort is possible.
Could you describe your scenario in more detail?
For instance, are you passively observing some computation and are trying to extract statistics? Or can you request that some specific code be executed at your direction and results provided back? Perhaps you could request specific hardware observations - how many nanoseconds after a particular bus cycle do address lines change state? In what sequence? Although hardware can be simulated as easily...
'Security by obscurity' can work if your system is big and computations are forced down your throat by a hostile party. Consider how your browser can be identified by fingerprinting. There are maybe 5 browsers you can choose from, created by corporations to collect data and allow web-site providers to collect data while distracting you with pretty pictures. They make sure that enough data is leaking from each request that you are easily and generally uniquely identifiable. Any attempt to anonymize yourself - by blocking cookies, faking your browser version, etc. is a joke
http://amiunique.org, or worse yet, can make you even more identifiable. In my case my tracking blockers leaked even more data than they were blocking!
So at least if you design an '8-bit internet', gain cooperation with network providers and dominant software vendors, and force each user to broadcast a fingerprint without them being able to do anything about it, maybe yes.