That indeed is the tragedy of the JMT in the last few years. It's so popular that it takes years to get permits, kinda like rafting the Grand Canyon. However, if you are persistent, you will get a permit.
No permits needed if you do it in the winter with nearly inevitable avalanches and subzero temps. Some crazy people have, not just the JMT but the whole PCT (the JMT is a subset of the PCT).