Use a bike and it's going to pick up wear and damage marks, mostly cosmetic as long as you deal with them before they get too bad, as martinf says. Some even like their bikes to show the wear, people do tend to be less precious about them once they are showing their use, which might be no bad thing.
However, when you put a bike together and get it set up for your use, it's easy to see where some of the wear will take place, cable rub, fittings, lock rub, luggage straps... and it doesn't take much time, effort or cost to do a good job of protecting those areas and saving yourself some future jobs. I use 3M helicopter tape, take some time with it and it's pretty much invisible.
I don't think any mudguards come with good mud flaps, or ever have. A few reasons for that, mainly that there's no consensus on what a good flap is, it may vary from bike to bike and/or be dependent on use. Get it wrong and they also increase the potential to damage the guard itself, so I'm guessing the guard manufacturers would rather you took that risk yourself. Plus it's an opportunity to demonstrate your own creativity. as a quick goole will show!