It was quite standard in the “old days” — I just read my mail in Emacs from around ‘78 to around ‘98 and filed my mail in directories all over my system. Mutt, elm, mm etc all worked this way iirc. I blame the arrival of the PC for the silo approach to apps in general.

As for simply delivering them to other directories: that’s pretty easy depending on what very agent you use (Postfix, qmail, sendmail etc). They are all designed to support that. It’s the clients that struggle.