As others have frequently told me, don't think too much about optimisation before you've put everything in. It really does depend on the scale of what you're looking to accomplish, are you making something on the level of perhaps half life with frequently changing scenes? If so, you probably don't need to worry about optimisation too much, if you follow standard practice for making scenes and adding nodes to scenes you should be fine for most game ideas unless you're doing something pretty crazy so you need to let us know what you've got planned.
Also worth pointing out since in your tag you mentioned Godot 3, Godot 4 release candidate has come out and stable will soon be on the way and that does affect performance just by itself, if you're brand new to Godot I would go out of my way to advise maybe learning Godot 4 is a good idea then when the upgrade hits officially it won't be a problem for you. I went through the pain of learning 4 from 3 myself and re-writing the code and I'm glad I did since I can benefit from the updates.
