which assets exactly are you talking about? Usually you want to create scenes and use the scenes in your world-node. Its not uncommon to have tons of nodes in your scene-tree, especially for worlds.
If you want a more organized approach you can create a scene-collection in your tileset and store scenes of your sprites in there. This allows you to place those scenes just like you would with tiles.
Such a question should be asked on the Godot Forum though