Did a bit of reading in the docs. Following was separated among several articles lol. Parenting your Control nodes(all ui elements are control nodes) to a node 2d wont change performance, you are just giving your ui to world space. It doesnt really make sense to structure your scene like that.

Control is not heavier unless you are doing some really wierd input handling in your gui

1. _input() is called on every node in the scene until it is consumed ("SceneTree.set_input_as_handled ( )")

2. _gui_input() is called second if the input is still unhandled and is special because it is called only when

-The mouse pointer is over the control.
-The button was pressed over this control (control always captures input until button is released)
-Control provides keyboard/joypad focus via Control.focus_mode.
Also similar to node: you only need to override _gui_input()

Control has a method accept_input() which stops the event propagation

3~ if the event remains unhandled then

_unhandled_input() is called.

Godot's docs recommend implementing gameplay input in this method to allow the gui to intercept events. Example: mouse click on a menu item wont propogate to actual 3d or 2d objects behind the menu, or if your menu pop up you can handle input through the menu. FYI if you overrode _gui_input() and its childed to a node 2d, _gui_input() is still being called.

Usually I only see people implement _input(event) for games like your space invaders. _unhandled_input is probably best for mouse clicks.

Theres way more specifics, here is some of the docs I referenced,

http://docs.godotengine.org/en/3.0/tutorials/inputs/inputevent.html#how-does-it-work
http://docs.godotengine.org/en/3.0/classes/class_node.html#class-node-unhandled-input
http://docs.godotengine.org/en/3.0/classes/class_control.html?highlight=gui_control#id1
http://docs.godotengine.org/en/3.0/tutorials/gui/custom_gui_controls.html#input
http://docs.godotengine.org/en/3.0/classes/class_scenetree.html#class-scenetree-set-input-as-handled