Email encryption in thunderbird currently fullfills one goal: It allows the user to keep a top secret information as save as possible, during transfer and on the users computer. This comes with restraints in usability: Encrypted emails are not searchable and in case you loose your key or the password to your key, the content is lost.
In the last year with the revealings of Edward Snowden a new use case appeared: People now want to use encryption on a daily basis to secure all of their mails during transfer to prevent mass surveilance. Keeping them encrypted on the computer is not always needed and could easily archieved with a additional file/folder/harddrive encryption. In this new use case, the current implementation of encryption in thunderbird is a threat to security, as people will decide against using encryption on a daily basis.
With the filter users will have the option to overwrite/copy/move some or all emails decrypted (e.g. in combination with move/copy):
“copy message to” “encrypted”