Does JME3 attach a unique ID to every element of a scene?

A Control can be added to any Spatial in your game, usually it is used for custom behavior - so using it to give your object a custom int ID is not it’s main purpose but it should do the job. Here is the general documentation on Controls. Since I don’t even have the SDK I am not aware how it works, but I assume you need to write your Control with the ID field first and compile it. After that I would assume there is a menu to add a control to a spatial. Maybe someone more familiar with the SDK might be able to guide you here.