My guess was correct, when memory is filled from the database, for example after restarting pihole-FTL, queries that were blocked after CNAME inspection are counted as blocked and again as forwarded to the associated upstream server. They only go once into the total queries, though, therefore the total percentage goes over 100 %.
I don't know if that is also true if memory is generated live or if that is really only the case when read from the database. I'll open an issue on Github. (Actually, I just found an existing issue about the same problem that didn't get much attention: https://github.com/pi-hole/AdminLTE/issues/1612)