As explained here:

Doors and windows now always cut out both sides of straight or round walls when they are parallel or tangent to them [...] To avoid changes in your existing designed plans, this feature will work only for newly added doors and windows, except for service hatches that will continue to dig walls if they partly cover the wall thickness.

This is exactly what you experienced, the niches you created with transparent boxes with Sweet Home 3D 5.2 are still here when you open your file in Sweet Home 3D 5.6, but the new ones created from the catalog (not the ones copied - pasted from the existing file) always cut out the both sides of walls. If you don't want this behavior, use a service hatch setting its material to transparent. You may still use the transparent box like in previous versions only if you include it in a sh3f file and set its [font=courier new]doorOrWindowWallCutOutOnBothSides#[/font] property to [font=courier new]false[/font] in the [font=courier new]PluginFurnitureCatalog.properties[/font] file, like in the DiggingInvisibleBox.sh3f file attached to this post.