It wasn't too long ago that I wrote about moving all of my e-mail over to Mail.app from myriad applications going back to '99. At that time, and as I mentioned in that post, I sorted the e-mail by year and sent/received. I've since gone the way of some others and removed the year from the equation altogether, so that now there are just two files: sent and received. These are not small files (14,000+ received; 11,500+ sent — not including mailing lists or school-related junk) and Mail.app has handled them without issue. Not once did it hiccup as I dragged and dropped mailboxes with 3,000+ e-mails into the main received box. In fact, I've yet to have any trouble whatsoever with the large files. The only real difference I've noticed at all is a slow-down in indexing time when you click on a mailbox-- it's trivial but noticeable. I was sold, until...
...I shutdown Mail.app and brought it back up. It was hosed. At least for a short while. For one thing, it took forever for it to "index" the files in the mailboxes — we're talking over 10 minutes. What is more, nearly half of the e-mail that was marked as spam (more on Mail.app's weakening spam detection in a later post), which was subsequently sent to the "Junk" folder, had reappeared in my inbox. I could find no rhyme or reason as to why some spams reappeared and others didn't. Given that these spams were now marked as "Not Junk," I had to go back through my inbox and remove all of them — manually — a daunting task when we are talking about almost a month's worth of e-mail (since the last time I shutdown Mail.app).
Given that the only real advantage to using the one-file-for-everything approach is the ability to search all of your e-mail at once (instead of searching through mailboxes by year or whatever other system you've come up with), the benefits no longer outweigh the risks if you're doing this with Mail.app; not when you face the possibility of having to weed out spam again and/or wait an indordinate amount of time to bring the application back up after prolonged periods of use.
I'm quite confident that Apple will correct these 'problems' in due time and will probably eventually move to the everything-in-one-file method where "virtual" folders are created using labels and whatnot (ala Evolution and now Gmail). Until then, I'm a little uneasy about having all of my eggs in one basket and might move everything back to the year+sent/received structure.