Provenance, provenance, provenance
Yes, many graded cards have been altered, and a common problem with graded baseball card collectors is many don't give one hoot, one care, where the card came from, just its current entombed grade. If they inquired, even insisted, on documented history-- even if merely having the seller of a gem mint card demonstrating that he got the card in that condition--, many alterations would be revealed.
The Importance of Provenance in Collecting