There is a new method in the .NET for Windows Store Apps:
Certificate.GetCertificateBlob()
It returns a BLOB which you can then transform into an array to get your byte array
// get certificate with given Friendly Name
var query = new CertificateQuery { FriendlyName = "certFriendlyName" };
certList = await CertificateStores.FindAllAsync(query);
Certificate cert = certList.First();
// get the BLOB of the certificate and transform it to byte[]
var blob = cert.GetCertificateBlob();
byte[] certData = blob.ToArray();
Also look here for more Information:
http://msdn.microsoft.com/en-us/library/windows/apps/windows.security.cryptography.certificates.certificate.getcertificateblob