1) I looked up the Sparkfun Pro Micro and it states to use the ATmega32U4 MCU. The datasheet found
here can tell you all about which pin has the pull up feature you need.
2) When a pin is setup as input with a pull up, then yes a switch connected to ground will make it read zero when closed and one when opened, but with the internal pull up being between 20K and 50K ohm you can have more problems with bouncing of the keys. This can be handled in software or by using additional capacitors and resistors to filter it externally.
3) Point to the explanation given and I might be able to elaborate on it. In principle there is no difference between them.
4) There is no need to express this in your schematic. The schematic just shows the circuit as it is made. If the schematic is also used for the software development without further documentation, then it would be beneficial to place some text stating the need for using the internal pull ups of the MCU.