It depends on what your use case is.
If you have well targeted queries (eg, with filters on "From" or "Subject" headers, and only query the message headers (not the payload) you can have a pretty good performance.
Most of my filtering would be based on the contents of the subject header. I have a site that sends me copies of particular transactions, and these few thousand messages are the ones I'd like to query. Ideally I'd like to have them downloaded for statistical processing.
What is your use case, exactly ?