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hi,
I am studying different metals in the presence of H.
To calculate H binding energy, I do the following:

binding energy1 = E(supercell+H) - E(supercell) -0.5* H2(molecule)
= -0.3 eV

Now, I am also interested in calculating H binding energy to supercell containing one metal vacancy. In order to do so, I calculate:

binding energy2= E(supercell+vacancy+H)- E(supercell+vacancy)-0.5*H2(molecule).
= -0.6 eV

My question is: can I compare these two binding energy to say that H binds more strongly to the system with one metal vacancy? Is this a fair comparison given the difference in the number of atoms involved?
Thank you.

yes, of course you can, because your binidng energy referst to different reference systems. of course you should keep in mind that the vacancy concentration might be unreasonably high as compared to experiment because of the possible supercell size.