There are multiple rate limits which have different points to which they count their rate limit. See Rate Limits - Let's Encrypt for more info.
In your case your main limit is the Certificates per Registered Domain.
That said, if the subdomains are delegated to multiple different persons, it's probably a good idea to have your domain listed on the Public Suffix List, e.g., to avoid privacy-damaging "supercookies" being set for high-level domain name suffixes. See https://publicsuffix.org/ for more info. A side effect of having your domain on the PSL is that the calculation of the rate limit for Certificates per Registered Domain is now calculated for the subdomains. Note that this is a side effect and you cannot use the LE rate limits as an argument to include your domain on the PSL.
Once my root domain (In my previous example : example.com) added in the public suffix file , will the subdomains (sub1 and sub2) have their own letsencrypt limits quotas ?