Not directly. You could talk theory for days (for example, 'balanced classes' being good - having a good mix of freshman/sophomores/juniors/seniors is better than 10 seniors or 10 freshman in your program, planning, etc.) about how it's a negative with regard to how your scholarships are used.. but, nothing directly.
The players are on one year scholarships. If a guy leaves, that's simply a scholarship you don't renew.
With regard to the APR... I think* the calculation is essentially based on (players in good academic standing + players staying in school) divided by (players + players that could stay in school)... 1 point for each player's academic standing and, if applicable, 1 point for retention of that player. If a guy leaves early to go pro, and is in good academic standing, the school get the point.. obviously they don't get the retention point, however, they are not penalized the retention point either. So, if you think of a player that is in good academic standing and returns, you'd get 2 out of 2 points, or 100%. If you think of a player that is in good academic standing and goes pro, you'd get 1 out of 1 point, or 100%.
So again.. not a direct impact.. but, if you have other issues in your program, not getting the additional 1/1 could 'hurt' your calculation mathematically.
The short answer is no. A guy going pro early doesn't hurt your scholarship count.