Hmm, hopefully later version of Godot adds option for project settings to keep tool tips processing even when paused.
I do not think there is pause function for nodes, and settings parent nodes process to false does not seem to affect its childrens...
Therefore I wrote this ugly pause function:
for i in Game.scene.get_node("YSort").get_children():
i.set_process(!pause)
i.set_process_input(!pause)
i.set_physics_process(!pause)
i.set_process_internal(!pause)
i.set_process_unhandled_input(!pause)
i.set_process_unhandled_key_input(!pause)
This solved the tool tips issue atleast ! Thanks