It's the same with the 3D boxes. In fact, I'm pretty sure it's the same with all objects. Once an object is added to your .cap, you can add as many instances of that object as you like and your filesize isn't going to go up any appreciable amount. It will a little bit, just for the information on where to place it, what UID it is, and such... but we're talking a matter of bytes.
Runtime is a different story, but as long as you don't have a metric crapload of 5mb .pngs with alpha flying around your screen at HD resolutions you're probably not going to see much in the way of a performance hit.
In other words, you don't have to worry too much about it.