Firstly, it's really cool that email headers are now encrypted by enigmail, including the subject. Very nice, thanks for the work!
However one side-effect is that References:/In-Reply-To: headers are now encrypted, meaning Thunderbird can't read these to arrange messages in the same thread together. This persists even after I decrypt the emails.
Optionally, it should be possible for enigmail to store this metadata locally after I decrypt the email once, so that the next time I open up Thunderbird the messages are still grouped together even though they are not decrypted in the current session. Of course this would be a security-vs-convenience tradeoff, but as a user I personally would opt for that convenience.
I'm aware of that issue. Consensus among the authors of the standard is to not protect those headers because of that reason.