There are a couple cases in which I could see a "snap-ring repaired" transmission being less reliable than a transmission that has not been repaired. The first is if the snap-ring broke due to the machining error, and the car was continued to be driven with the broken bits floating around in the trans fluid. These bits could damage the gears or bearings. If not replaced, this could cause problems down the road. The second way I could see is if the transmission was not rebuilt correctly. It's possible that one of the bearings could be damaged during the process if not pressed off or removed correctly. If the bearing was not replaced, or any of the other items that are in some way removed during the repair not installed correctly, this could cause a problem down the road.
However, if done correctly, a snap-ring repaired transmission should be a *better* transmisson than a from-factory transmission with some wear and tear since most techs doing the repair would recommend that bearings and syncros be replaced since the transmission is on the bench.
On a side note, keep in mind that many of the cars I have seen with transmissions that have been repaired do not have the cases marked in some way by the tech signifying that the transmission has been repaired for the snap ring TSB. Since the affected case half is not the one with the transmission number, if not marked, the next owner could be under the assumption that the trans has never been repaired w/o supporting service history.
take care,
-- Chris