I think you must have noticed something slightly different. The max aperture is a function of the lens and should be unaffected by camera.
The Nikon 60mm Micro AF-D will change its maximum aperture as a function of the focus distance. As it focuses closer, the reported max aperture drops. By life size 1:1, its down to f/5.
There is apparently a button on the 50mm AF-D that will lock it to its minimum aperture. This is a property of manual aperture lenses. Modern cameras control the aperture automatically from the camera body. Setting this switch locks it at the minimum aperture so that the camera can automatically control it. Since your camera has an in-body focus motor, you're able to use the AF-D or AF-S, you just need to decide if there's a difference for the price that you care about. They'll both take great pictures, the AF-S will just focus faster and quieter mainly.