I tend to group sites into CF accounts based on topics or themes for domain names which is just a personal preference. You can lump all sites into one CF account too.
One valid reason to separate domain sites to different CF accounts is due to CF Domain Registrar billing/auto renewals which don’t have the best invoicing/email communication so if you have many domains in one CF account and domain registrar auto renewal comes up, you may find it harder to figure which credit card charges relate to which domains as not all CF email invoicing/billing list the domain it’s auto renewal charge is for. Then you can setup email filters based on CF account email the emails are sent to.
See my feature improvement request at Domain Renewal Notification/Confirmation Emails - Add domain name