This is not correct at all. Spatial is not "the parent of all 3D nodes". On the contrary, it's the simplest of 3D nodes. It has a small number of properties related to position and orientation in space, and that's it:
What you may be confused by is that all 3D nodes inherit from Spatial. All 3D nodes have Spatial properties. That means a Camera is a Spatial node, a KinematicBody is a Spatial node, etc. This is how Godot is designed to work. You're going to need to use 3D nodes if you're going to do things in 3D.
I highly recommend going through the official tutorials, in particular:
- Step by Step - introduces the editor, node hierarchy, and overall "Godot way" of doing things
- 3D Section - several good tutorials here, including working with 3D nodes and building an FPS game
On another note, when you're a beginner worrying about performance is the very last thing you should be doing. Make something, then worry about whether there's a performance issue if there turns out to be one. Odds are, especially with the very small projects you'll be doing as a beginner, there's not going to ever be one.