Ok I think I solved it.
Before reinstalling from scratch and restoring config backup, I gave this a try :
sudo du /etc/pihole/pihole-FTL.db -h
DB was 1.5Gb
sudo pihole flush
sudo systemctl stop pihole-FTL
sudo rm /etc/pihole/pihole-FTL.db
sudo systemctl start pihole-FTL
sudo du /etc/pihole/pihole-FTL.db -h
DB is 92K
Now pihole CPU usage is back to something acceptable and GUI is browsable.
I lost the log though 
Credits to this Reddit thread : https://www.reddit.com/r/pihole/comments/1iss62l/pihole_v6_extremely_slow_gui_high_cpu_usage/
And this page :Free Up Pi-Hole Disk Space Usage
Thank you all for looking into this.
Hope this can help others.