5 3's a game from Cooney means teams pack it in the paint and Rak's effectiveness declines. Patterson could probably play a few minutes at SG, but that means G has to be at PG and BJ has to be in the game at SF; we can't have Joseph and Patterson in the game at the same time because that limits us to just 3 possible scorers. BJ at SF, G at SG, and Joseph or Patterson at PG is a lineup I can get behind. it would require BJ to play strong enough defense to stay on the court though, and it also wouldn't get rid of the 'player shooting too many 3's' problem.
Again, limiting Cooney's 3's to 5 or so per game also means we're taking away the games where he shoots near 40% at a high volume. I know these games aren't common for him, but they're not ultra rare either. You could argue that he should keep shooting if he makes 3's early, but what about the games where he misses his first 4 but hits or could hit his next 3? Sure, he could miss the next 3, but you'd never know. It's a tradeoff. He's in there to shoot and Boeheim trusts his ability to shoot. That's enough for me.
Another factor that's not being considered, is that Cooney puts up this many shots in essentially 40 whole minutes of play. I'd say it's a safe bet that we can knock down his average 3pt attempts by 1.5 or 2 per game, scaling it to the amount of PT most starting SG's see.