It likely would make it easiest to assign force-field coefficients. If you had a situation where you had 2 different molecules but shared atom types between molecules, then it most likely would make sense to share atom types. But in your case with H2O and H2, you most likely want to have two different H atom types, if your force-field assigns the H's different pair coefficients, for example.
I have a very stupid question for atom type. For example, I have a structure of mixed water and hydrogen molecules. Since the potential parameters for H in H2O and H in H2 are different, I think these H atoms need to be set as two different atom types. Am I right about this?