Yep. An ordinary round hole punch worked, but you could also get a purpose built punch that made a nice rectangular notch, had a guide to get the position just right, and had more leverage making it easier to punch through the thick jacket. "Dual sided" floppies (with two factory cut notches) cost enough extra that the tool paid for itself pretty quickly, IIRC.

Of course, the floppy manufacturers warned that the cheaper single sided floppies had only been tested on the front side, and might have defects on the back. But I don't remember that ever being a real problem.