yeah but you can pull a website for almost any fault, on any car if you look hard enough. There are plenty of perfectly working SMG BMWs running around the world, but of course you will never hear them complaining on the internet that its still working OK.
If you're buying a E46 with SMG, and you are worried about failure, why not just take out a warranty and just drive the car like its meant to be driven? SMG IMO is NO reason to completely discount a car, unless you specifically want a tractor box to make you feel more manly. The rear subframe issue is a much bigger problem, but even that wouldnt stop me buying an E46 M3, just make sure its thoroughly inspected and reinforced/fixed.