Pen drives are electric where most external HDD's have spinning disk and require more power.
Unfortunately with the Y cable and my old GC controllers, I do use all four ports at once (Y cable and two ports for GC controller adapter). I hope I don't need to plug anything else into the USB ports! But this also means if you want to use the new style GC controllers for Smash, you can only use two of them at a time (via USB connector) if you are running Smash from the HDD, plugged in with the Y cable.