The borg needed his command codes. Assimilation would not necessarily recover encrypted data and may even alter how data encrypts and decrypts by the usual Borg upgrade process.  "I understand that you have no interest in me, that your goal is access to the encryption codes for the enterprise computer!"
   He would also be upgraded, and possibly reprogrammed, which would likely alter how he encrypts and decrypts, and may actually make him more problematic as he would be a Borg upgraded Soong type android!
   This makes sense if then data is also encoded in a relativistic rather than absolute fashion, relating data to other data (see Marvin Minsky's frames theory).
   Locutus says, specifically, that Data will be obsolete in the new order.  However, technically, he does have brain scans of a great number of scientists and was stated in one episode to have improved one of his systems, so who knows what he would become!  I do not believe they cared, but we do.