How come objects are invisible in certain viewports? For example i want to select things using the top view, but probably 80% of my scene cannot be scene in the top view or even clicked on…
What kind of objects? -> e.g a plane is pretty difficult to see from the top down view 
Here are some screenshots of perspective view vs top view. All objects.
Far away objects are probably clipped by your far clip distance of the camera. Try enlarge the far clip distance of the camera. Also z-fighting may be a culprit here.
And how would u adjust the far clip plane of an orthographic top camera in the editor?
Also fun fact… when i hit the button at hte upper right to give me 4 views (top, side, front and perspective) The issue no longer exists… very very strange bug there.