Authentic Japanese swords were equipped with only one pin. This should be enough if the handle has been made properly (with maximum friction around the nakago).
However, should a samurai have felt that his sword handle was getting loose, he would simply have his sword repaired by the village sayashi (saya-maker) and tsukamakishi (handle wrapper).
In current times, replacing a sword handle can be a very costly job and not every city has craftsmen in this area.
For this reason it can be a good idea to have two mekugi pins. Practitioners do not always have the experience to locate, recognize and repair the problems of a sword. A second pin may just save your own or someone else's life.