Finally I found out how to bring my Thunderbird back to speed. The extremely simple solution was to move all e-mails out of my inbox and create a dedicated folder for those that I want to keep. Simple and effective. Now Thunderbird is fun to use again
EDIT: I should also mention that I have tried several alternatives, like claws-mail or KMail and while they are definitley good mail clients they did not provide the features (especially live virtual folders) and stability I was used to from Thunderbird.