Black knot is caused by the fungus Apiosporina morbosa - you might also find it listed with an older name, Dibotryon morbosum. The disease is well-named because of the large black galls on twigs and branches. It is definitely worth trying to prune out the infection. This is quite a bit easier if the knots are on twigs or smaller branches rather than on major limbs or the trunk. Prune about 2-4 inches below each knot. If the knot is on a major branch that you want to save, you can still attempt to cut out the diseased area - try to get down to clean wood and beyond the edges of the gall by 3/4 to one inch. Prune when the tree is still dormant as the fungus, which survives in the knots, will start producing new spores about the same time the buds start to break. Try to keep your pruning shears clean - I periodically spray and wipe pruning tools with rubbing alcohol. Some people also like to apply a fungicide spray to the branches, such as lime-sulfur, in the early spring to knock down any new spores. You should scout around nearby to see if there are any wild plums or cherries that might be a reservoir for disease. Wild plums are quite a bit more susceptible than cherries.