The Custom Domain limit I believe is 100 per domain/zone (but if you’re on Enterprise, I’d bet it could be raised), and there is a documented limit of 1,000 worker routes per zone.
Why can’t you use worker/http routes then? You can set up a wildcard DNS Record AAAA*.domain.com100::Proxied and then a wildcard worker route like *.domain.com/*. You can do that on deeper subdomain as well, as long as you buy Adv. Certificate Manager (ACM) and issue a wildcard certificate.