Practically speaking, it also makes using and querying that data and doing any kind of analytics much, much more expensive. It is done that way in some cases, but in the absence of a technical requirement to do so, there are cheaper approaches.
Those are solvable problems. I could also argue how address space separation and more generally MMU protections make things so, so much more complex (they do!), yet we don’t question that one very much.
There is no end to end encryption involved here, so you don’t need to resort to such voodoo as homomorphic encryption.