I suspect it's more of a grounding or shielding issue than the frequency used multiplexing all the LEDs. If it were due to an abnormally low multiplex frequency I'd expect to see some strobing of the LEDs on video clips of the guitar in action, but you can't see that on any of the videos. I get very similar whining noise on any of my (non-Fretlight) guitars when plugged into the audio interface on my PC while running amp sims, but the difference is that I can move away from the PC or change my position relative to the PC to minimise the severity of the noise, whereas in the Fretlight the noise-inducing electronics are a permanent fixture that you can't get away from.
There is one item on their FAQ page which suggests that noise is a known issue with the system, and that correct grounding is key to eliminating the problem (or at least making it tolerable). It appears to be mentioned in the "Troubleshooting" section of product manual too. On the flipside, there do seem to be plenty of videos of people using the guitars with lots of gain but no apparent noise issues, so I guess the noise can be tamed. It's a shame that it appears to be prone to induced noise, because I can see a lot of people would benefit from the system when starting out, and the guitar could act as a crossover point when transitioning between absolute beginner to live performances.
To be fair, it is marketed as a training tool rather than a performance instrument. Perhaps going the extra distance to install a piezo pickup and full modeling system would push the price up to a point where the target market wouldn't be willing to pay for such a product?
Either way, you've done an impressive job marrying the two systems together