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If you are showing Available actions (as it appears you are), the only way a project or action group should show up is if all of its items are completed, or there aren't any. The notion is that the project or action group shows up only when the work is complete, to indicate to you that it is time to either add more actions or mark it complete.

There is an option to hide the parent items: use View->Hide Parent Items in Context View to remove them from view. Unfortunately, there's no way to specify the state of that option in a perspective, so you'll have to turn it on and off by hand if you want it on part of the time. If you think this would be a useful option to add to perspectives, use Help->Send Feedback to send in a feature request to the Omni developers.

One workaround that comes to mind if you have projects that are frequently empty, but you don't want to hide all the parent items: add a dummy action to the project with a start date far in the future.