A solution is available on reddit.
cd /etc/.pihole
sudo git fetch --unshallow
cd /var/www/html/admin
sudo git fetch --unshallow
than run pihole updatechecker local
refresh the pihole admin page, the update notification did disappear on my system.
if you disabled the pihole cronjob pihole updatechecker local that runs every 10 minutes, enable it again.
If it doesn't work, there is a possible other solution described in the reddit article.