Your deleted messages are in a folder shown in the left-hand column of Thunderbird. It may be called Trash or Deleted Messages, depending on how closely it matches Hotmail.
Normally, rather than erasing "deleted" messages, it shifts them into this special folder, just in case you hit Delete accidentally.
Right-clicking on that folder should show a menu which will have an item called something like "Empty Trash". Using that will clear out all those messages you have deleted.
With so many years to deal with, it may take some time to tidy up. There will then be another period while all those removals are replicated to the Hotmail servers.
