Why is it difficult to include water vapor in a graph that shows the percentages of various gases in the atmosphere?
Quite probably because the percentage of water in the atmosphere is a function of temperature.
Given a temperature, the water vapour content of the atmosphere is known. These are extensively tabulated. When a gas is collected by bubbling thru water and displacing a volume of water in say a graduated cylinder, the saturated water vapour pressure must always be used to make a correction.