Would I hurt/break my Denon receiver (5.1) if I only plug in 2 or 3 speakers

You will not hurt it unless you also hook up cables and cross +/- where you don't have speakers (but I'm not thinking anyone with enough know-how to use the internet would do that)

LCR is probably the most preferred 3-channel set up. You get good soundstaging and an enhanced theatre viewing experience.

The vast majority of Denon receivers (I believe all) have RCA out for sub. Your receiver's amp isn't being used at all to run the sub if this is the case. Now, if you are talking about running an unpowered sub off your rear channels, you're over my head.

This is exactly what the thing is designed to do. Don't plug in unused wires and run the setup, and you should be enjoying better sound in no time.

No.

Been running mine this way since 2013.

I refuse to crawl through blown insulation to run wires.