There is a lot of misunderstandings around messaging systems.
End-to-end encryption is an extremely nice feature as it lets us make the assumption that messages cannot be read by a middle man even if 100% of the employees are corrupt and the messages pass right through FSB and NSAs networks twice.
But, as you point out: for most people this falls flat in most cases once you are up against the big guys and they have decided to get you.
That does not mean that it is useless though: most people won't get approached by these agencies, and E2E-encryption will keep it out of the hands of dragnet surveillance, snooping telecoms providers or FAANG companies and a number of other very realistic scenarios.
(That is unless you use a system that helpfully uploads unencrypted copies of everything you write to a certain large FAANG class company.)
Then there is federation, I guess that is what you mean by decentralized. This is another really sweet property of a messaging system. However, for security it has a number of problems - a little bit less or more depending on exact implementation.
On top of this there is technical execution: Everyones (including me) darling Signal for example has had some pretty nasty problems.
Alltogether it comes down to this if you want to avoid problems: stay out of what trouble you can stay out of and think opsec if you cannot.
And remember that US knew exactly when Soviet started working towards an atomic bomb, because after they started the flow of related research papers stopped ;-)
I.e. opsec is seriously hard if you are up against a powerful entity. Plausible deniability, blending in etc can be just as useful as bulletproof crypto.