Most tutorials start out with 2D content for a reason - because 2D is easier to deal with when you're learning. Much of Godot's nodes work the same way in 2D and 3D. For example, the official 2D tutorial shows how to detect two object colliding:
The physics introduction gives more detail about the different types of collision nodes:
In 2D, you'd make the cubes
Area2D nodes and connect the
body_entered signal to detect the player picking them up. In 3D, the node is
Area, and everything else is the same.