It is legitimate (though mostly futile) to question the wisdom of conventions. For example, a more logical spelling of the word "could" would be "cound".

Key signatures are conventions of notation, not of the music itself. A key signature of just Eb and Ab would make perfect sense; if the music contains any Bb, a flat accidental can be added at the note. The ABC notation language used at Mudcat actually allows for such signatures: "K:C _e_a" or "K:Cm =b" - try them out!

Nevertheless, they are nonstandard, mainly for reasons of history ("musica ficta"). But I also doubt that they would make for improved logic (as "cound" would).

Again: this is only a matter of notation. Scales and harmonies of minor keys are different topics, quite independent.