In normal storage, AF vs. MF usually makes little difference. Many photographers leave the lens in AF because it can keep the focus mechanism from moving as easily, which may help prevent the barrel or focus ring from shifting in storage. On some lenses that are not full-time manual focus, forcing the focus ring while set to AF could potentially stress gears or the AF motor, but this is unlikely in ordinary handling.

So the practical answer is: either setting is generally fine, with a slight preference for AF if you want the focus mechanism more "locked" during storage.

As for leaving the lens on the camera: that’s generally fine and often preferable unless you have a reason to remove it. Keeping a lens mounted reduces unnecessary lens changes, which helps minimize dust getting into the camera body. If you do store lenses separately, use the proper caps.