Absolutely! It's perfectly ok to salt the beans when cooking. In fact, it adds more flavor and doesn't keep them from fully cooking. The myth of salt interfering with cooking has finally been debunked (#6). Most of the time, if beans don't cook correctly, is because they are old or you have hard water (acidic water). Be sure to source beans from a place that replenishes them often and try using purified water or add 1/2 teaspoon baking soda to the water.