I recommend you check out this topic: I figured out how to create components without nodes (and it is much better!) The author creates a good use case for using Resources instead of Nodes for use in composition.
Ultimately, the choice is yours. As you make your game(s) you will find places where a Resource works better than a Node. For me, I use Resources the way I would use a Struct in C or C++. Basically I use them as ways to store complex data. They have advantages in that there is a built-in way to save them to disk. It’s also a good way to share the information between objects.
I use a Node when I want to know that something exists as part of an object by looking at the node tree. For example, I often hang Timers off other Nodes even though I could just create one in code and put the time in an exported variable. I do the same thing with my StateMachine and State objects. They actually could be much simpler objects, but I find that utilizing them as nodes allows me to immediately see what states an object has without diving into the code.
Ultimately, I don’t think it’s about “missing” anything. Knowing about them allows you to make design choices. For example, I had a bear of a time saving keybindings to disk using the normal FileManager. So I converted that code to save as a resource, and it became very easy to implement.