I just tested on a brand new clean install of v1.3.9d, and added the demo products, and browsed down to cPath=3_10 where there are several products. I then went into the Admin area and marked 3 of those products as Out of Stock (red dot). When I go back into the store under cPath=3_10, those 3 products I marked as out-of-stock no longer show in the New Products for July section, and of course they don't show in the product listing above either.
I even added some brand new categories with multiple levels, and disabled some products in the bottom level, and the disabled products properly disappear from the New Products centerbox.
The problem is not "a zencart issue".
It's a problem with the custom code you're using to display your customized New Products centerbox section, which is pulling products from the parent category (above the current one) regardless of status, unlike the built-in original New Products box which pulls only enabled products from only subcats below the current one.