You want to support HTTPS requests on your application that contains more than 100 custom domains.
The 100 domain limit is not unique to Heroku or Let's Encrypt. Most certificate issuers limit certificates to 100 domains due to historical browser limitations and performance reasons.
To support more than 100 domains with SSL you'll need to separate your domains into groups of 100 and purchase a SAN cert from a provider covering those domains. You cannot use Automatic Certificate Management (ACM) for this.
For each certificate you'll create a separate applications with it's own SSL Endpoint add-on. Here's more info on that approach: