No, Fourier Analysis is not a theory. It's a theorem; it can be shown to be perfect with math. Unless you can show a fault in the actual math, all of your hand waving and word salad is for naught.
Fourier Analysis, as a theory, is a subset of Harmonic Analysis theory. It has dozens of theorems. If you are interested, pick one of these books - Harmonic Analysis on Amazon - and see for yourself.
A handful of the theorems is routinely used by DSP practitioners. For instance, Parseval's Theorem can be used for quick estimation of THD contributed by a device, via comparing pre- and post- waveforms.
Again, I'm an analog guy. But if we seek better digital, it can't be done without understanding how digital works. I'm all for hi-res and everything it takes to get the best out of it. But let's not pretend that somehow the underlying premise of digital audio is somehow broken. It isn't. Its problems are elsewhere.
One of the problems, as I see it, is simplification, excessive popularization, and at times even vulgarization of science, which became widespread in the Western world during the several past decades.
I guess I have to go that route as well, given the circumstances. So here it goes. A mathematical theorem is like a part of a legal contract: its words have precise meaning, often unexpectedly different from their everyday meaning; and it has small print.
As it relates to the Sampling Theorem, the phrase "contains frequencies" means something quite different from what everyday common sense would make one assume. And the theorem itself is just a paragraph in a long contract, with lots of small print.
Let's say you have a health insurance contract, and it covers your teenage son too. He rides electric bicycle. God forbid, he gets in an accident on the bicycle, hits his head, and requires expensive urgent care and rehabilitation.
Naturally, you assume that the insurance will cover it all, and you feel safe in belief that you'll be only out for deductibles and copays.
Suddenly, your insurance company sends you official letter saying that this event isn't going to be covered by them, because during the accident, according to a police report, your son was violating The Law.
Perhaps he was riding without a helmet. Perhaps he was riding on a walkway in a town with an ordnance prohibiting that. And there is a small print in the actual insurance contract stipulating its provisions null and void if injuries were sustained in the process of violating The Law.
As it relates to the Sampling Theorem, the signal has to fulfill very precise obligations, before the theorem can guarantee its accurate capture and reconstruction.
The meaning of the words describing these obligations is precisely defined elsewhere in the theory, in other definitions, lemmas, and theorems. Nothing wrong with the theory per se, at all.
Practical music doesn't fulfill these obligations, and thus the Sampling Theorem only works approximately. How well it works can be calculated too, using other parts of the theory, yet this is far more involved, and the answer is signal-dependent.
The vulgarization, in the case of CD format marketing, was in omission of the facts I described in the previous paragraph. Was it done on purpose or through honest mistake? I don't know.