Not necessarily. That presumes that the entire chain of balls is sticking one short of the expected position. That may be possible. It's also possible for the balls to be stuck together in one or more clumps, each of which may or may not roll fully to where the trough optos expect the balls to be. And then those balls may shift around at weird times. Basically a series of pseudo-random (unpredictable) things that can lead to problems that "occasionally rear its ugly head without warning", as you note.
I'm not saying that everyone who has unexpected problems with the trough, crazy ball saves, etc can 100% blame magnetized balls. Tons of issues -- mechanical, electrical, software -- could be involved, and if you're having trouble, the American Pinball team is standing by to help you. But if you are experiencing trough-related problems, by all means, please pull out the balls and test them to see if they're magnetized. If they are (even a little bit!), it is highly recommended to switch them out for balls that aren't magnetized, and hopefully that simple solution will resolve your issue.