I agree with you here 100%. Maybe this is a good pathway to explaining why relational databases are good ideas in much the same way as having a programming strategy that uses a backbone of pure functions. This purity-dividend is exactly why the relational model is such a good strategy for database management.

In the same way haskell lets you separate your pure functional code from your monadic code, giving you the ability to referentially transparent reasoning and construct imperative machines where you must, the RDBMS approach applies total logic programming to database management. It's frustrating because your code cannot all live in one language as it can in Haskell, but the separation of pure from impure is exactly where the value is coming from.

RDBMSs focus on values and total computations (you know they will halt, making it even easier to reason about queries than non-total functions) allows you to isolate simple logic programs from the rest of your impure non-total code.

Navigational databases don't give the same benefits because they are not value based nor are they total. They are the imperative-model of the database world, and though they are easy to write, they will end up difficult to debug, maintain, and keep coherent.