It is perfectly fine.
And legal.
Almost every used ball I’ve ever owned has had this done, and only ever had the fingers crack out on one of them.
I’ve got an original black hammer from 1987 that I plugged and redrilled the thumb on in 1988. Moved the thumb 3/8 inch and redrilled, leaving a partial plug.
Still throw it at spares, and it has never given me any problems.