Google is in the process of making improvements in this area. Soon you won't have to add HTTP, HTTPS, and different sub-domains separately. Google announced that it is working on being able to add a domain:
... users need a more comprehensive view of their website and so we will soon add the option of managing a search console account over an entire domain (regardless of schema type and sub-domains).
It isn't clear exactly when that will happen. Google is retiring the "property sets" feature in April and I'm hoping we can start adding domains around the same time that property sets go away.
Until then, you either need to ignore the emails, or remove the HTTP property. If you are sure everything is migrated to HTTPS properly, there shouldn't be much value in having the HTTP property around anymore. It certainly won't hurt your site in any way to remove the property. You just won't have access to historical data or be able to use it to look for additional problems.