I'm not sure if anything happened to his dad, I think he just wanted to start using the Jr. part to honor him for all that he did for him to help him reach this stage in his life. I imagine it was partly sparked on by the fact that there were 2 receivers with the last name - in other words he used that situation to honor his dad rather than doing it simply to clear up any confusion for uninformed/opponent's fans. I know they never added the Moniker Jr. to his name while at Tech, they probably would have on senior day when the two would be introduced at the same time but he left early (I'm not upset about that as he could have and probably should have gone to ugag where they had a competent QB to get the ball to him, so I'm just grateful he came for a year let alone 3).
Also in terms of the video game it is necessary to have an extra qualifier for one of the Johnsons, for example: I'm currently playing the Lions in my Packers dynasty, and I'm on defense its 3rd and 20+ yards I know the best player in their receiving corps is Calvin Johnson, problem is from the pre-play screen I can't tell which of the 2 Johnson's I need to key as the numbers are too small on the screen. You see where it would be difficult to know which one is which if they both just had Johnson. By the way as soon as I saw Jr. I hit the key and what do you know the pass went to him he picked up about 15 but he's still 10 yards short, If I would have chosen the lesser Johnson he might have been able to slip through the cracks. It's necessary and since he's expressed interest in going by Calvin Johnson Jr. there shouldn't be any problem. I just call him CJ (what's cool is I got to shake his hand during his freshman year at the "great Jacket encounter" during a time when nobody but the scout.com followers knew who he was, he was just wondering the halls, 2 games later and he was a Legend at Tech)