You can search primary address using filter like (mail=JohnDoe@foo.com), but similar filter (proxyAddresses=johnDoe@foo.com) won't return anything. This is because attribute "proxyAddresses" holds not only smtp addresses, but also other types, e.g. RightFax, X.25, as well. To search secondary smtp addresses, you need to define a filter like this
(proxyAddresses=smtp:johnDoe@foo.com)