It's always good to have second source, and I bet mil spec certification is a pain in the rear, they require more than one source for everything and their tolerances make everyone suck it in =) Guess it depends on really what your goal is in the first place. Simply trying to outsource the same filters from another company or two may be possible. doing them in house may be as well. I'm not a filter expert, in fact it's probably one of my least knowledgeable areas in electronics, but you can reduce inductor requirements (hence size) by carefully chosing the rest of your components and the actual filter topology.