I don't think there is anything special about the qmail maildirs other than the fact that each message is stuffed in its own file. I think the main advantage with qmail maildirs is the locking method that qmail uses guarantees that mail messages don't get lost or corrupted.
As far as processing each individual message, any library that implements mime encoding/decoding will probably work whether its written in java or tcl or whatever. Look at how the java code currently processes a maildir file. It just reads it in and passes it along to the javamail package. No special qmail related processing is done for the message file.
In the openacs webmail module the java code is only used for access to the javamail api which does the mime encoding/decoding. It would be quite easy to replace this code with something equivalent written in tcl. As a start you might trying searching the dev.scriptics.com site to see if a mime library module already written in tcl exists.
