While I have trojita running (in background and not) if I try to open trojita, it opens itself another time. It does not happen, e.g. with kmail. If it is opened, when I try to reopen it, it does not do anything.
Yes, this is planned and a proof-of-concept is already written, but not merged yet. It will be needed for proper mailto: URL handling, among other things. Agostino, Trojita (as the upstream project) is managed by more developers than just me, and I'm the only one of them which lingers on Gentoo's Bugzilla. This particular feature was written by Pali during his GSoC work, and is waiting for a couple of finishing touches before it gets merged. Could you please file these feature requests at KDE in future? That way, all of Trojita developers will be aware of what we managed to break :).