I think the Junior A issue now will be recruiting/retention. I am tied in with a club and know almost every kid on the roster has a goal of getting to NCAA at some level. Agents and Advisors will now push for those players to get to the CHL level as thats the route to getting an NCAA scholarship now. Will it only affect 3-4 players off each Junior A team....likely you are right there. But the kids that dont have a shot at the CHL ranks, and knowing full well they will have a much smaller or almost no chance at an NCAA scholarship playing in Junior A leagues will just decide to get on with their lives and go to university/college instead.
Junior A is not cheap for players at all anymore, decades ago players got paid to play and provided with everything they needed throughout the year. Now with Player Development Fees, league fees and some teams charging billet/transportation fees most players are paying $3000-$10,000 a year to play and that doesn't include any additional expenses such as vehicles, spending money, trips home etc. So as a parent, I won't be spending thousands of dollars for a kid whos not CHL bound to play a few years and end up in college/university a few years behind their friends. That money can go towards their education....not hockey for fun.
Also you have to think along the lines of scouts/coaches from the NCAA, where are they going to look to find players. If you can now scout/recruit from the best league in North America, which also includes going to bigger cities, nicer places and have less travel/better accommodations, are you going to travel to Nipiwin Sask for a less talented league in hopes of finding a gem, or are you going to go to do a BC swing and hit Kelowna, Vancouver, Lethbridge and Calgary? I know NCAA coaches who's gone on recruiting trips, they very much already avoid going to prairies as much as they can because the product isn't as good as well as who wants to spend a week in a car going from small town to small town.
I foresee several Junior A clubs closing up shop once all this hits, many of the community owned teams struggle to make ends meet already, and if the on ice product diminishes....it will be harder.
Also....top end talent in the CHL will still go the pro route, but how many of the CHL top end talent walk right on to a NHL/AHL team at 20 years old. Not as many as we want to believe, if your 5th round draft pick isn't quite ready for the pros yet, most NHL clubs will say....hey we can get you on Michigan for a couple years. Then we can re-assess after some more development.