Taking care of your Mac (put into a sleep or shutting down)
I have a Macbook Air but I'm going to assume it's the same in Apple's laptops.


Yes, though unplugging a MacBook overnight won't drain much of the battery. It shouldn't overcharge/damage the Apple adapter will make sure of that.
Yes, you can store it vertically when you have it closed. It's okay to rotate any laptop with an SSD in it as long as you keep it away from being bumped or falling over, or really strong magnets. Bumps and falls may not damage your SSD, but it could affect your laptop's functionality.
It is totally idle, operations will resume once you open your MacBook and re-login (if needed). Though you may see some notifications when you open your MacBook, I assume these are notifications before your MacBook entirely goes to sleep. So don't worry about it making any notification sound when it's closed, I keep mine that way and haven't noticed any notification sound. The notifications are from sent to the Notification Center when you Login, the app that send them check the time, and if they would have sent them during the PC was asleep then they do what they were intent to do e.g Calendar etc. The PC does run maintenance script though they make no sound at all, also it can back up to Time Machine, if you have that on. There are few more things that can run, if you have Power Nap enabled (Energy Save Pref Pane).