This emphasizes the fact that they aren't normal text. I used small caps for other acronyms. After trying various possibilities, I decided to leave RUNet alone, i.e. to leave it as full caps and lowercase. In my paper, I repeat Bringhurst's position. He, and I, prefer the en dash.
Some people have strong preferences here.
However I looked through my books on typography and found just about an even mix. The goal is to produce a visible separation, but one that doesn't disrupt the even appearance of the page.