I don't use caps because that's just another thing to unthread and lose on the side of the road. On a bike, stem caps are superfluous, unless you have like LED flashing acrylic dice or something. That's cool.
I removed the dork disc when I changed out my cassette, because it's as superfluous as valve caps. If the RD is adjusted correctly, that disc will never do anything except get destroyed by the sun and clang around on your rear wheel.
I didn't need to remove the reflectors because the bike only came with two, and they weren't even installed. I do run a blinky front light and a 2W taillight at all times. Reflectors do indeed serve a purpose, but I ride in daylight hours, so they won't help me.