You should consider the Mk XII Adapted MACO gear and both cutting beam and Omega Plasma torpedo launcher before making your final decision on turning in you BNP's. Also take into account, the set bonus of the Cutting beam, Plasma launcher and adapted console. It can be pretty cool.
Well, I didn't have an option besides the one to turn in Omega Marks for dilithium (though I do remember seeing the BNP project at one time now that I think about it.) Maybe something is borked.
I seem to be one of the few who have a serious shortfall of Omega Marks while I can get Romulan Marks by the ton. I tried STF's and they just didn't jive for me and if I have to hack one more drone on Defera, I may have a psychotic episode. (As an aside - that might make an interesting FE.)
Anyway, I really don't have the desire to harvest the massive amounts of Omega marks required for the Mk XII gear when it's only marginally better than the Mk X, so the BNP's are pretty much useless to me.