do military sims count towards civilian instrument rating? i know military flight time doesn't.
Why are you even worried about this? After you get your wings, you just go to the FSDO and take the military competency exam. It's a written test covering things like FARs. After you pass, you get a commercial instrument ticket for whatever you flew. For example, fixed wing guys usually get single and multi-engine airplane while helo guys get helo and single engine airplane (from their T-34 primary days). Just be sure to do it right away as you have to have flown the aircraft you want the license for within a certain time period. We had guys in my P-3 squadron who did not get the single-engine rating because they were too long out of primary.
If you quit or flunked out of flight training, you would have to have had a military instructor who also had a civilian CFII to count the sim time toward an instrument rating. And he would have had to make and sign a log book entry for you.
Edit: Posted the above as you were posting that you are a NFO/SNFO. In this case, the instructor would have to have the civilian CFI or CFII rating. If this is the case and he was willing to sign a civilian logbook entry, you can count the sim time and the stick time towards the appropriate ratings. I don't think many military instructors are civilian ones though. In one of my P-3 squadrons, we had a PPC who was a CFI/CFII/MEI. He used to let NFOs fly during the transits under the hood and would sign their civilian books so it counted towards their ratings. It was just time building for all practical purposed because he could do no real training. He took a few into the 2F87 and did instument training there for them.