Your ionic version command gives u the version of the ionic command line interface
The npx cap gives u the version of capacitor cli
These versions are different and not comparable. So you cannot say 6 is better because it is higher than 3. Apples and pears
Next, Ionic cli invokes the capacitor cli under the hood. So with ionic v6 u run capacitor v3
You can use both to achieve the same.There can be comfort sticking to one cli interface for ease of reference and potentially (but not very likely) version issues