The two 3.3 V pins are linked internally on the Pi, so linking them on the Black HAT Hack3r would be unnecessary in most cases. It’d also make the routing look ugly, since it’d involve via’ing through the board and running a trace from one 3v to the other and… well, rats to that!
The 5V are conveniently next to each other, and we almost always use a ground plane for ground- IE the whole area of the board that isn’t part of another trace is all one big ground wire so ground is always universally connected. So the grounds being connected is, I suspect, more due to convention than intent.
I can see how connecting the 3.3V pins on the board would be useful, though! Since it’s not always desirable to use a whole ribbon cable… in fact I hate ribbon cables.