Or perhaps you need to revisit your decision to require "many subdomains" and consider whether it's a sensible decision if it relies on somebody else providing SSL certs for them inexpensively or for free.

You can buy a wildcard cert for under a hundred bucks these days - how much obligation do you think LetsEncrypt have to change their product to save you $100/year because of your design decisions? If LetsEncrypt (or Namecheap) don't work for you, pay someone who sells a thing that _does_ work for you (or change your requirements).