Question
Do the bores in the tree itself affect the fruit so you can not eat the cherries even though the cherries look perfectly fine??

Answer
No. Insect borers are in the woody cells of the tree trunk (sometimes the limbs) and are not in the fruit. There are insects that will feed on the fruit but you will be able to tell by the damage on the fruit. If there are signs of borer activity on the tree trunk the fruit will not be effected. I would however control the borers they can over time kill the tree. Spray the area on the trunk with an insecticide called Merit. This will kill the insect in the trunk. Check with your local nursery fro this product. There are products that can be applied to the soil to kill borers but I would not use them on fruit tree since the product may be transported to the fruit and make it not useable for food. The spray will not have any effect on the fruit and would be safe to use on the trunk.