I know this is an older posting, but figured I would bump it up in case others are having issues.
Here is the situation with my setup.
New install with basic settings. But I am using the Bootstrap 4 template and have the navbar setup.
Everything is setup fine and I am actually using a direct URL to the shop (whether I use a direct url or choose from the list, the output is the same), but the output uses a hashtag instead of the actual URL.