Hate to necro such an old thread, but being that I just ordered a single 12" upfire box from Zenclosures and I do have the rear cargo shade I was wondering the same thing. I suppose when it comes in I'll find out whether or not I can still use it. I'll post some pics once it comes in and I test fit it to confirm.
Edit: Some pictures
Here.
Anyone looking to put one of these in with the rear cargo shade, I have disappointing news for you. It's gotta go. No way to fit that in there with one of these boxes.