How do doctors treat a small hole in the roof of the mouth under the skin? Will there be any major side effects? What are the Causes?

Tricky. cannot say in your particular case, but generally, the AREAS of gaps in the roof of the mouth are deforming and need surgery (CLEFT PALATE). Without an exam, cannot say much: 1) these occur at birth. Problems from birth if they don't cause problems by adulthood probably won't. 2) but can (uncommonly) occur with other birth defects, but again, lung/skeletal/ear problems would have shown.