Had a 3040, 3050, 3350 and a 3650 in the past and never had any problem with brakes or transmission, and the 3040 left the farm with12k on the clock. As far as I know the likes of the 6200’s were more prone to the brake linings breaking up
In theory if the brake discs brake up then the broken pieces should be caught in the hydraulics filter. Normally the brakes are in the rear axle so unless jd share the rear axle oil with the transmission or vise versa then it is virtually impossible for any disc fragments to get in the transmission. They are also in the oil to keep what would be dust if they were dry off the discs and therefore keeping them smoother an therefore the brake work better.