Hole in tree
They might be from insects. One of the holes look like it could be an emergence hole from an insect (borer) with frass (insect fecal material) still in the hole. The picture is in focus (awesome) and close to the holes which is why I think it could be from an insect. Unfortunately, I am unable to guess as to which insect it is partly because of the picture.
How old is the tree? A mature and established cherry tree can have different texture to the trunk while still having lenticels. Without seeing more of the tree, I am not sure which insect it could be because I am unsure it is a cherry. Could it be a different tree with a weeping growth form? A picture showing more of the trunk (cherry trees have lenticels as part of the bark usually) or of the entire tree may be helpful. A cherry tree, or other Prunus species, that has suffered borer attack (this type of insect) or a wound often exhibits gummosis and I do not see any in this photo. Did the tree ever have sap-like sticky substance oozing out of the trunk? Did you ever see anything looking like sawdust in the crotches of branches or at the base of the tree.
Correct tree identification would be more critical for future issues if necessary. I suspect it is a cherry tree, as you say, but it is best to be sure for identification purposes. A cherry tree with these holes could have suffered an attack by either peach tree borer or lesser peach tree borers (day flying moths). A bark spray of either bifenthrin or permethrin (active ingredients of the insecticide) would be needed to protect the plant. These can be found at box stores or garden centers in the area.