On my end, the menu never uses short links regardless of permalink setting. However, when viewing a Wiki with a list of pages, the page links there use the s/ shortlink.

When trying to add a wiki page directly to the menu, it doesn't show up at all (seems to be a separate bug).

The minor issue is the s/ is preceding the normal wiki/ URL when following links from the menu or the tree. The s/ isn't needed in that context imo. My installs are always special, somehow.