Data breaches are considered "immutable", that is they are unable to be changed as they reflect an incident at a previous point in time. Email addresses cannot later be removed from a domain, for example as they belong to staff no longer working at an organisation (there's also no publicly available information to ascertain which addresses are no longer valid). The only way to remove an email is for the owner of the address to use the opt-out feature and select the option to permanently remove the data from HIBP.
The total size of a domain is also the single practical metric we have available to calculate the subscription tier it belongs to. Knowing the total size of the domain over time is a key component of assigning it to a commensurate product.