I use Emacs' rmail with mairix as a search tool. I can link to emails via rmail like this:

  [[rmail:<mbox-path>#<message-id>][link text]]

No need to type that out, M-x org-store-link does that for me in any rmail buffer.

I split my mboxes regularly, so I need to link them via mairix instead of rmail. I haven't set it up yet, but that is so trivial I guess it's already done.