Is there a way to make a short ID/name for a note, and then add a fairly long note – invisible – inside the note box? If not, I fear that a few notes will fill up the screen.
No there is nothing like that in Scapple. One of its design principles is that your notes should fill up the screen, and even go beyond the screen! It’s meant to be used the way you would use a blackboard—everything on the surface, with nothing hidden from view. If an idea requires a lot of space to express it, then the software should be “honest” about that and not allow you to hide it or use a smaller amount of space than precisely how much it takes to express it. It may require you to think a little differently about how you visually express information—this is expressly not an outliner or a mind-mapping program, where hiding the amount of information it takes to express a concept is baked into the very principle of their design, from its viewing models to the idea of having a “heading plus data”.
In recognition of the fact that one shouldn’t be constrained by the size of their computer monitor, we hope that you find our navigation tools to support this philosophy. You can for instance hold down the ‘Z’ key to view your entire board at once, merely point at a spot you wish to examine more closely, and let go of the key. You can dynamically zoom and pan the board around as well. As you build outward, the board will automatically expand as you go, so there is no need to worry about making the “blackboard bigger”. 
Hope you find these tricks useful.