In a healthy tree this will rarely be a problem. Any damage to the bark (cutting off branches, drilling holes, etc) carries a risk of infecting the tree. A healthy tree is essential as it can heal quickly.
You should bear in mind that over a few years, the tree will grow and the bark will swell round the eye of the bolt and eventually absorb the whole thing - although this is not harmful to the tree. This will also mean the bolt will become nearly impossible to remove as the bark grows tightly around the threads, even if you can undo the nut at the end.