Sadly, no, but you can remove and re-insert on the tree.
Instanced scenes can be marked as placeholder in the editor (the instance node drop down menu), so you can add them to the tree but won't appear until you activate them by instancing (this can work like a "disabled" GameObject for testing too).
Is like a PackedScene but with the instance location already placed on the tree, then instance the node with
May be possible to replace it back to a InstancePlaceholder but not sure.
More options, add many
Node as placeholder, then
replace_by the node/scene you want, disable it by replacing it back by a
Node (Node2D/Spatial if you want to keep the position), you will need to set again all the signals and groups.
Pause mode may work but is global, is better to use to pause everything except a few nodes (like a pause menu).
All the methods that affect the tree (with node replacement/re-insertion) will execute
_ready (godot 2-) and
_enter_tree again on the node when re-entering.