They will be resized automatically when created in maps, but not when created in other views — big notes in that case could expand to make it hard to place them. You can adjust their size whenever you like with Note ▸ Expand Proportionately .
Is there a programmatic way to do this? Can I have an agent regularly call this on all notes? My notes’ names are short and I do not use composites (I have turned these off via $NeverComposite=true), so if two notes now touch or overlap that is not the end of the world for me.