Its probably because the M3 SD was more expensive to develop or just because the hardware is more expensive. Just because its older doesnt mean it wil be cheaper.
What makes it that expensive is the 256 mbits of ram. Slot 1 card don't have that. It is the main reason. The M3 SD pro doesnt have that and is a lot cheaper.
Even the m3 cf ( if you can find it) still cost a pretty penny, probably more than a slot 1. Luckily it's still a great card and works just fine. Add the fact that with an old f2a and wrg dumper it can dump ds games properly.