The position, length and form of a tone hole will determine the intonation and sound character of the particular note. The shape of it can be rather complicated. Besides the note for which it is meant to be, it can also have a significant influence on other notes. Finally, it is very important, that it is perfectly airtight when closed.
The quality of the tone hole is therefore very important. Any damage will automatically have a negative influence. Even on brand new instruments it is common for damages to be observed which ought to be fixed.