In an ArcGIS Pro layout, it is not possible to disable the layers in a map frame without affecting the same layers within another map frame if they reference the same map. Any configuration made to a layer is reflected in all the map frames that reference the same map. To display different map layers, create a copy of the original map and modify the copy as needed. When creating new map frames in a layout, select different maps as references to each map frame. This workflow is useful to highlight different layers in different map frames.
The image below shows the Parks layer in Map 2 (the copied map) is disabled without affecting the Parks layer in Map 1.