It has been a long time since JJY was on SW but they may have used something like two beeps/second there.
You don’t usually see AM or CW keying on VLF though. The antenna BW (because they antennas are so short compared to the wavelength) is extremely small and it becomes difficult to build an efficient antenna that has a BW wide enough to support AM modulation.
On-off keying (CW) is also difficult, particularly at power. I think JJY is a 50 kW station. Keying a large load on and off is hard on the electrical system and the power supply. Still, from what I read JJY does send a CW ID, so they apparently do that. WWVB uses a modulation scheme that raises and lowers power.
Most VLF stations today use a MSK. It is efficient, has a constant carrier, and works with antennas with narrow bandwidths. I don’t know what JJY uses but MSK would be my first guess (and I emphasize that I am guessing.)