You're overlooking one thing, though. Microphonics aren't the only thing to consider in the vibration of the pickup. Since the pickup signal is a result of the string moving through the pickup's magnetic field, relativity dictates that the signal is also a result of the pickup's magnetic field moving across the string. For example, if you could shake a pickup side-to-side across a stationary string 440 times per second, the pickup would generate a signal of an A note.
So even if you play a single note on a guitar, the vibration of the wood will vibrate the pickup, the pickup and its magnetic field will vibrate across all six strings, and this will be added to the final guitar signal. Whether it's significant enough is debateable but there is more than just inherent pickup microphonics to consider.