As far as I've seen, the 3D is incompatible with most if not all HDTVs. The big issue is that the way they de-interlace and refresh does not sync properly with the glasses. As far as aftermarket glasses go, though, yeah, modern shutter stereoscopic 3D glasses with a 3.5mm headphone jack will work with the card slot adapter, but you'll still need that component.
These are the Sega-branded glasses, and the second picture shows the card slot adapter, which syncs the shuttering with the video coming from the Master System. It is fully compatible with the Power Base Converter as well.
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