I would just make sure that my horses were up to date on their vaccinations for every possible disease, and probably more often than normal on the ones that are airborn or mosquito-born like Flu, Rhino, Strangles, and West Nile and Encephalitis.
Well, I'm thinking all this over for what to do as policy in our own boarding stable someday, and I think the answer might that I vaccinate them myself, all together, and just bill the boarders.... I don't know how else you enforce vaccinations on people's word and memory about whether they are up to date on everything.