He appears as an unlockable player in NCAA Football 14's Ultimate Team mode, which lets gamers add certain real-life names to their teams by completing challenges in the Skills Trainer mode.
The decision to include the former All-American tight end was surely made well before the investigation into Odin Lloyd's murder first made news on June 18. And the game's July 9 release meant the game didn't have much of a window for removing him. Based on player and team ratings leaks, the game looks to have been finalized before June 11.
Update: EA Sports' Julie Foster comments:
We made a decision to remove Aaron Hernandez from Madden NFL 25 and NCAA Football 14. Because NCAA Football 14 was finalized prior to our decision, Hernandez' image still appears in the Nike Skills Trainer. However, he is not in the game, and anyone who unlocks that particular Nike Skills Trainer reward will receive an Alex Smith Ultimate Team player item instead. The image of Hernandez will be removed via a Title Update in the near future.