В крайна сметка просто преглеждах масива:
Schemas.Client.findOne({ _id: id, 'customers._id': customerID }).select('customers.$.addresses').exec(function (err, client) {
if (err) { return next(err); }
if (!client) { return next(); }
if (client.customers[0].addresses.length) {
var addresses = client.customers[0].addresses;
for (var i = 0; i < addresses.length; i++) {
addresses[i].isDefault = false;
}
client.save(function (err) {
if (err) { return next(err); }
// finish
});
}
});