If by “folder” you meant an entity to group its (2D) children, and affect all their transforms at once - yes, it’s normal, that’s what are nodes made for.
If you want a strictly logical hierarchy - you may use just Node instead.
Usually, Node2D is for nodes that will be instanced in other scenes. Node for the main line.
This is normal. Make a heirarchy:
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Add functions banner(name) and menu(name) that turn on the visibility of the selected menu and all others off. This gives you an easy way to develop the gui in the gui editor and choose when to see it in code.