Seeler, my son is a Sophomore at a D1 JUCO as well and has pitched only 1 inning this year due to early season shoulder soreness that took half his season away.
It can be discouraging for the boys but it is my belief that things happen for a reason, and all we need to do is to continue encouraging them to keep their heads up, work hard, and make the best of their situation for the remainder of the season. At the end of the year if your nephew's team is fortunate to make the conference playoff's, typically there are quite a few scouts that attend these. Encourage him and/or his parents to try a decent collegiate summer team to play on. You've heard the others above say that the 4yr schools are now assessing their pitching needs for next year and after the season it will ramp up even more due to exit interviews, transfers, draft, etc.
My son, while disappointed that he didn't get to have the big season he was hoping for this year, is now looking forward. He realizes how strong his arm will actually be this summer and sitting around 92-93mph he is actually going to see what opens up with teams while having fun on his summer team. Could virtually missing this season due to the injury be a blessing in disguise? Dunno. But that's how he is having to look at it now.
Help your nephew begin looking at the silver lining instead of worrying. Jemaz is correct in that worrying will accomplish nothing at all.
Good luck.
YGD