Need to support thousands of unique SSL certificates on a single VIP

As such there is no limit as per RFC. It will depend on CA.

From an implementation standpoint, many certificate authorities limit the number of SAN domains to as low as 25 entries to as high as 100, as per following link:

https://social.technet.microsoft.com/wiki/contents/articles/3306.pki-faq-what-is-the-maximum-number-of-names-that-can-be-included-in-the-san-extension.aspx