Cutting just the long roots off wouldn't be a concern if anything they will help as ppl actually do it if they aren't having clogging issues with root pruning...
You could always get the cc bulkhead filters too the 2 & 3 are the same btw..Just need one per bucket that's on the rear of the bucket that goes to the pump and problem solved...I use them on veg and bloom and wouldn't run it w/o even tho bloom is 3in but can still get clogged...
Also if your afraid of trimming the roots you could always just put the ends at the top of the root ball and do it that way...
I pry wouldn't rely totally on the airstone in front of the bulkhead but it does help but def not a fix well from my experience anyways..
And you wouldn't need to do less time in veg which would also lower your yield ...As for more root more fruit ....So less root will be less fruit...Since you would need 64 bulkhead filters I would contact cc direct and see what kind of deal they can do for you if not try one of their distributors I know of one here that would do a great deal on them if your interested in that route..It would give you the most peace of mind anyways and wouldn't have to worry about a bad clog or several and could kill the plants and water would be everywhere too granite that Pry wouldn't be a issue for you but would be a hassle and a total waste of money down the drain...
Glad you got the issue figured out though I imagine you checked all of the buckets to afterwards right on if there was any other clogs or real close to being ...b.h filters are def thee way to grow that's for sure