How to delete iCloud storage Mail cache?
I found a solution to my problem. So for future readers:

Mail is caching (Bug?) the storage space in Mail. So after deleting a few thousands E-Mails, the space is still taken.

The solution:


  Insert a few E-Mails back in archive. After importing a few E-Mails
  again, Apple is updating the cache.


Guide:


  
  Deleting every E-Mail in archive
  Spotting that the space is still taken
  Insert 3-4 E-Mails back to archive
  Waiting until the space is updated (look at iCloud.com)
  Deleting the 3-4 E-Mails in archive