I think you have it backwards. If they didn't switch all pins it would defeat the purpose. I suppose if the box were made after serial modems died out then it could omit the ring indicator (pin 9) as a cost savings measure but in all the AB-Y boxes I've taken apart they switch every pin. These switches do not put both peripherals in parallel with each other, but rather connect only one device at a time to the output.
There seems to be a misunderstanding here. This may be true for something like an IBM PC joystick that plugs into an actual RS232 serial port. Joysticks for systems like atari and commodore are entirely passive devices and do not utilize any type of communication protocol. Most every AB-Y box like the one you linked to will be entirely passive as well. The only similarity between a 9 pin RS232 serial devices and a 2600 joystick is that they both use a DE9 connector. DE9 is technically the correct name but DB9 is more commonly used.
I suspect most of the folks around here that game on actual hardware don't mind unplugging a controller and putting it away when it's not in use. It's kind of like unplugging a cartridge and plugging another one in, isn't it?
If you can find an AB-Y box that switches all 9 pins then your idea will work. Be sure to use a straight-thru cable between the AB-Y box and the console, not a null-modem cable. Also know that the metal connectors on this or any switch box will chew up the ends of your joysticks because they have dimples around the inside edges.