I know 4 (I think?) people with prosopagnosia and maybe 800 people total, so my first guess is 0.5%. Wikipedia says 2.5% and the internet says it's difficult to determine the true prevalence because many people don't realize they have it (generalizing from one example, I assume). The observed prevalence in CFAR / MIRI is something like 25%?

So another plausible hypothesis is that rationalists are unusually good at diagnosing their own prosopagnosia and the actual base rate is higher than one would expect based on self-reports.