I was referring to using the SegaCD's PCM audio system, not the Yamaha chip for square and triangle.I don't think you could use the square-wave channels to do the NES's pulse channels for two reasons: one, the NES has adjustable pulse width where the Genesis's chip does not, and two, the Genesis's chip, in the grand Yamaha tradition, uses logarithmic volume levels where everybody else, NES included, uses gradiated volume levels.
The NES only has 4 square wave duty cycles and it's easy to simulate then as wave samples. As for the NES volume being not logarithmic, I had run into this problem when emulating it on a logarithmic volume audio unit and used a simple lookup table for the differences.
Basic emulating of sweep, envelope, count length (and the linear one for triangle channel) isn't very hard or resource intensive either. Some of the clocks for those effects are twice per frame(1/60) but I had no problem doing them once per frame (skipping a clock cycle like frame skipping).