I bought an '87 Ninja 600R (ZX600b) and can't figure out whats missing that goes in or over this hole.
Is it missing a plug, a hose, or something else?
Is it important?
There is a hose that connects your air box to this
As stated in comments, this is connection point for a PCV hose. The hose connects to the bottom of your air box that attaches to your carburetors.
This hole allows for crankcase ventilation. Any gasses that should not be released into the atmosphere can be vented here. It should get pulled back into your motor and burnt, which is why it's connected to you air box.
There are additional emissions related components that are related to this ventilation system including a vacuum diaphragm.
See part number 90259D (Breather)
I think the hose is attached to the bottom of the air box you removed to get that photo. The connection point is very clean and the cases aren't covered in fresh oil. Just old stuff. Look on your air box and I think you may discover the hose that attaches to crank vent is attached to the air box and that you aren't missing any parts after all.
The Breather fitting is missing according to the diagram, you can buy one on Bike bandit.
Original OEM Part number was 92005-1129
Also it looks like 92005-1017 may be a tube that attaches to it, but not sure, schematics are not that good. You could call BikeBandit on the phone to figure out what is missing.