I sometimes used to supervise undergraduate dissertations through the process of agreeing an NDA with an industrial partner company. The university's internal IP team would usually carry out the initial drafting of the NDA. The university IP team's draft would invariably subject students and academic staff to restrictions onerous enough to be damaging to the dissertation process and to the student's subsequent graduate job search. In every case (*), it turned out that the industrial partner company did not particularly want those onerous restrictions, and was happy to agree to my request that they be dropped from the final version of the text of the NDA. In your case, the NDA is already signed, so that ship has sailed. However, my experience leads me to believe that, if you and your supervisor ask the company to release you from the requirements of the NDA for a particular publication, there's every chance they'll say "yes". (But make sure to get that "yes" in writing, and from an officer of the company who has legitimate authority to say it.)
(*) At least, in every case for which I was supervisor. Some colleagues in my group supervised projects for which it was otherwise.