Will my baby breastfeed less due to the blisters in his throat?

Yes. If your baby has any blisters, you should take her to a pediatrician immediately. With very young children there is always a concern for disseminated herpes infection which can be dangerous. Any type of mouth lesion in an infant can cause a decrease in feeding and possible dehydration.
Yes. If your baby has a throat infection, it may cause him to be less interested in drinking milk. If he has already been examined and is not thought to have anything more serious, a dose of Acetaminophen as recommended by your doctor may help to alleviate the pain. Sometimes feeding smaller, but more frequent amounts may be better to give your baby a break, but to maintain hydration.