To communicate your collisions back to your main node without putting code on your bullets or enemies.... for that, you will need signals.
Your bullets will need collision nodes, as will your enemies. You could use your bullet object with a child of Area2d, and the Area2d has a child of collision. Don't forget to set your collision shape. Do the same setup for your enemies.
Now use your signals, like "body_entered", and point them back to functions in your main node for evaluating those collisions.
Here's a great video on explaining signals which should be a big help: Introduction to Signals in Godot (tutorial)