I do face this issue now and then after updating sailfish and/or whatsapp. I think it has something to do with me having android data and /home/nemo mounted to sd card. (correcting the mount --bind to mount --rbind mostly fixes the issue)
What helped back on sailfish ver.1.x.x was:
-backup Whatsapp data only (using titanium backup)
-remove whatsapp
-restart aliendalvik
-start Exdialer and let it load all contacts
-restart aliendalvik
-reinstall whatsapp but dont start it
-restore Whatsapp data with Titanium backup (data only)
-start WhatsApp and check if contacts load again