[rodw]

It is absolutely possible (and effective, depending on what you consider to be an adequate ROI) to apply this sort of heuristic to this domain.

The "holy grail" of a universal AMT that works with any number of instruments of any type played concurrently isn't exactly an intractable problem to begin with, but if you constrain the problem in various ways (to specific instruments, to known tunings, etc.) you can definitely take advantage of a priori knowledge about the "timbre" of the instrument and the way in which the sound wave evolves over the duration of the note/notes to work-around what would otherwise be more ambiguous data. The octave/harmonics problem is one example of the kind of problem that is much easier to eliminate (relative to the abstract case) if you can make assumptions about the type of instrument that is generating the sound.

The overtones generated by the vibrations of a guitar string (for example) follow a fairly specific and distinctive pattern. If you dig a little bit into the physics/mechanics by which a given instrument generates sound there is a lot of tell-tale information to take advantage of.