CSS Zoom does not work iPad OS (v13- latest) Safari
I see your issue. Unfortunately, I have noticed that Apple has broken several aspects of webpage rendering on iPadOS, leaving several minor visual quirks that didn't exist in Safari 12 for iPad.

Although it is very annoying that they broke Safari, unfortunately, we have to live with it in the meantime. What I would do is create a script that will increase and decrease the size of the elements, text, borders, etc. when you change the "zoom" size. Doing this would also give support for the Firefox browser, as it doesn't have support for the CSS zoom.

This suggestion might not be ideal, depending on what you are trying to do, but hopefully, this helps somewhat.

Also, it should be noted that the iPadOS Safari browser's built-in zoom feature using a keyboard will work correctly, just not the CSS zoom.