When Apple locked down the System volume they made it impossible to change things on the System volume. Thus the built-in international fonts used for language support cannot be disabled nor removed as in the past. Fonts you add to the system will be kept in the Data volume and you will be able to disable those fonts.
As to Apple apps not showing all the fonts, they are likely filtering based on the current language in use. When showing a fonts in the inspector view you will see the languages displayed. Affinity apps are showing you everything. When browsing the fonts in Affinity Apps there are several tiny filter buttons at the top, All, Recent, Used, and Favorites. So you could mark the fonts you want to use as favorites in Affinity and when you filter on Favorites you will only see the fonts you marked as one of your favorites.
Going further, you could submit a feature request explaining the desire to filter available fonts based on the system language as a feature request within the Affinity forums. It would likely be useful for other language speakers beyond English. https://forum.affinity.serif.com/index.php?/forum/52-feature-requests-suggestions/