I don’t know the source of this statistic, so please correct me if I’m wrong, but I suspect this impressive statistic comes about because of inherent bias in the data used. I would guess that what is actually meant is that 40% of documented extinctions in the last 400 years are non-marine mollusks. And this (again I’m guessing) is largely due to the fact that non-marine mollusks leave behind copious shells that can be IDed to species even if the species was extinct before it was described scientifically. And those shells have so many amazing details that it is easy to find traits upon which species delineations can be hung. So I’d guess that the great majority of extinctions in the last 500 years have been organisms humans will never know existed. If we were able to split nematodes into species as easily as mollusks, and they left behind as many clearly identifiable remains, we might be saying that the vast majority of animals going extinct in the last 500 years were nematodes. The same might be said of mites.
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