On the first issue you point it right, I scale icon sizes in Caja to 100%, 66% and 50% so the issue is only on 66% on default theme Ambiant Mate.
The 100% setting in Caja displays 48px icons (I don't know if it tries to adapt to 96 with HiDPI − I doubt it as most icon themes don't provide such big icons, but it's possible that they're upscaled on the fly from 48). 66% would be 32px and 50% 24px. Which would fit with the issue of missing 32px size for some icons in Humanity. All the ones I have checked in the CC have 48px and 24px (some also have 22px and/or 16px).
So icons in Control center have to be reworked to have a consistent size.
As I said, it would be an upstream bug: the MATE themes (Ambiant & Radiant) only include icons specific to MATE (green folders, apps like Welcome, the Software Boutique, Caja, Engrampa...). The remaining are loaded from the Humanity icon theme which is designed by Canonical.
In any case, the solutions from Ubuntu MATE's point of view are a bit limited:
- make the Control Center display icons at 48px rather than 32 (might feel too big);
- make the CC downscale icons from 48px to 32 when they don't exist (will be blurry);
- make a full icon theme rather than rely on Humanity, which would be quite unproductive.
The proper solution would be to file a bug report for the Humanity theme so that all the appropriate icons get additional sizes and hope that the Canonical designers do it before the next century (barring that they don't just dismiss it because "Ubuntu will get a complete new set of icons starting with next version, as we said each year since 2006, but this time it's true!").