None of the journals I work with will accept any format other than .tex or .doc for submission, its pretty ridiculous. We totally rely on the journals to distribute information but they have no incentive to optimize the process for reproducability or ease of use. Don't get me started on publication fees and access fees.
We're getting around this by putting a paragraph at the end of the conclusion with a link that says something to the effect of "Click here for a live version of the paper with all the code and data used in this project." It's a little more cumbersome than having the paper actually be the notebook but it helps.
