Now, with your help, I have more information.
In fact, the vaccinaton, although "encouraged by Napoleon, was far from being really efficiently performed among the soldiers (the idea that the Grande Armée was vaccinated at Boulogne is a myth). According to the Dictionnaire Napoleon, after a recommendation signed by Percy and Coste, and with the support of some marshals, only.... 59 men were vaccinated, in 1806-1807, in Bernadotte's Corps d'Armée, 66 in Davout's one, 500 in Sout's and, at the beginning of 1807, only 2066 soldiers were vaccinated in the Grande Armée ! Around 1815, this number was triplefolded, but this was still a minimum fraction of the army.
But the vaccination was more efficient in the populaton, whereby, between 1811 and 1815, 50% of new born were vaccinated. The number of smallpox cases was, at the end of the empire, about 25% of what it was before the Revolution.