Using coordinates for connections is simple and adequate. Why would that be dumb?
I once bought a program that did not (always) delete netlist connections when you deleted wires in the schematic. That was real dumb and a one way ticket to the garbage bin.
I'm hoping that KiCad will one day get a reverse (engineering) workflow implemented.
That way you would start by a few photographs of a PCB, draw tracks over it in the PCB editor, then port the netlist to the schematic editor, and use assistance of the ratsnets in the schematic to draw the wires in the schematic.
A function like that would require a smarter way to handle connections, but for now this simple method is adequate.