There's a saying that I'm about to butcher by paraphrasing, because I can't remember it precisely. But it's something like Theory works in practice, in theory. In practice, it's a little more complicated. I take issue with your argument for two reason. One, a pickup's magnetic field isn't that narrowly focused. It picks up string movement along a certain length of the string, not at one specific point. So even if someone did play a harmonic exactly over the center of a pickup's pole, the pickup would still pick up vibrations further out from where the harmonic is happening, so it's never entirely "deaf."Having studied the Physics of musical instruments at a university - getting my degree in Acoustical Physics, I have to disagree. Harmonics do indeed exist (on strings, in rooms, in pipes, and other places) as "standing waves".
A simple demo can easily show this - pluck the 5th harmonic on a 50's style P bass (which has it's pickup ne fifth of the way from the bridge to the nut. Theory predicts that a pickup located there will be deaf to that harmonic. If you try it, you can hear it acoustically (that frequency is absolutely there on the string, and radiating into the air), but if you listen to the output of the bass, it isn't there - it's listening at a node, and the string, at that frequency doesn't translate there, so the pickup doesn't hear it. It's real, it's Science, and its easily demonstrable.
Two, whatever a bass's tone is at any given moment, it continues to sound like itself all the way up and down the neck as you play it (with the exception of the occasional dead spot at a certain fret, which is related more to the wood of the neck than harmonics). People who have found that quintessential P sound they've been looking for, still have that sound regardless of where on the neck they play.
Please note, I'm not disrespecting your education or trying to argue that harmonics don't exist as standing waves or anything like that. I just don't think the specific placement of a pickup has that much real-world effect -- moving it a quarter inch in either direction isn't going to do much.