Hi again Brad. You're welcome, I'm glad to offer what I can.
Yes, 90dB S/N isn't likely to result in much audible noise. I don't think the Casio will ever be that good, but I have two suggestions which may (or may not
) help, if you haven't tried them already.
The first is to experiment with the output volume setting of the WK-3000. I would try turning it up, and the sound card line input volume correspondingly down. That should help if the source of the hiss is the output amp section of the Casio. Obviously, don't turn the Casio up to the point where the sound card input is overloaded.
The second is to make sure that the sound card mixer level control for the microphone input is turned down or muted, assuming you aren't also using a mic while recording the Casio. Mic inputs are notorious for being noisy, often especially when left open circuit (no mic attached), and a lot of the software mixers for sound cards default to having the gain turned up and unmuted for all inputs. In fact, it wouldn't hurt to make sure any input you're not using is turned down.
I'm assuming that the cable from the Casio to the sound card is a shielded cable. That's important because the high-frequency noise from digital circuits can sometimes cause hiss-like sounds, and although the output impedance of the headphone circuit is relatively low, there might still be something picked up.
I hope that you find a solution in what I mentioned. Otherwise, NR and gating may indeed be the answer. Good luck.
--Barry