This is actually a long-standing bug which Volition found out about way back in FS1.
I think it was discovered in that mission where two transports evacuate a Faustus science vessel. In any case, the mission designer mentioned a Faustus and trying to dock two things to it at once, reported a bug, and Adam (I think) tried for a few days to fix it before saying it was simply too messy to fix, and enforced the one-dock limit. Some of the details may be wrong in my narrative here, as it was 4 or so years ago. I think this info was originally posted to either the FDL or FUDL, so it might be floating around in their archives.
http://www.descent-freespace.com/ddn/ (see "Mailing Lists")
You'll notice that many of the models (fs1 models especially), especially some of the shivan freighters, have multiple dock ports. When the models were originally designed, there was apparently no knowledge of this limit.
I do remember uncovering a very unusual bug (in FS1) involving these dock limits when trying some combination of docking multiple transports to a Fenris. I think it involved having one transport initially docked, and then having another one dock and undock. (I really don't remember the details...) In any case, when some combination of docking-related things had occured, the fenris went FLYING OFF at THOUSANDS of m/s! (The first time it ran over my ship, instantly killing me, and leaving me saying, "WTF?" Took another try before I found out what happened.) Switching the camera to the Fenris showed the sky absolutely thick with those little debris particles (apparently there is some linear relationship between speed and the number of particles you see.)
So, um, yeah, it'd be really nice to fix this, especially for those freighters that are designed to be docked to multiple cargo containers.
Another idea I had (back in the fs1 days) was to have a jump platform for fighters. You see, in fs1 (before the last few missions, anyway), fighters didn't have jump drives capable of inter-system travel. So I thought it'd be nice to have a ship that many fighters would be docked to (like a spine, or something), and would have an inter-system jump drive, so that an entire destroyer wouldn't have to jump in to a system just to deploy fighters. It's not a carrier, exactly, because its far simpler than that. I think I-War has some similar thing, but I never really played it, so I donno.
Of course, in fs2 time frame, this is all sorta moot. All the ships can do inter-system jumps now.
(Hm, that's a whole lotta ramblin')