The obvious difference is the number of certificates - and hence load on Let's Encrypts system / services ( which is one of the reasons for the rate limits).
From an SEO viewpoint I don't think there is any difference. For some ( e.g. domain and www.domain ) I have them on a single cert. For other subdomains ( e.g. special_function.domain ) I have it as a separate cert, since it's independent in function ( and often on a completely different server ). It's all a mater of personal preference.