I haven't looked at "chaplaincy" emphases within MDiv programs in a number of years. But from back when I was keeping tabs on these "tracks" within an MDiv program...
They tend to focus on counseling at the expense of Bible/Theology/History.
I think this is terribly misguided. There are some great men in the chaplaincy, but a lot of them lack the necessary rubric for processing today's troubles in light of Biblical truth. A significant number of chaplains are woefully lacking in terms of ability to do real Biblical exegesis and theology... so preaching in military chapels is legendarily weak (not just in biblical content, but in homiletic ability as well).
This is in part because people go into the chaplaincy thinking "I'll do a lot of counseling, so I'd better prepare by taking a lot of counseling courses" and while they are prepared to do the "counselor" part of the job, they are woefully unprepared to do the "religious services provider" part of the job. (I friend of mine got an accredited MDiv from a school that required no language classes, and only 2 Bible classes: an OT survey and a NT survey, and 1 class in theology... the rest was counseling related. And even though I do consider him to be a friend, I have to say: his preaching and teaching are abysmal because he simply doesn't have the knowledge base.)
Here's the thing: whether you're prepared or not, if you go active duty you're going to be baptized by fire into the counseling world. You will rapidly gain a lot of experience. The military will provide you with a number of training opportunities - even certifications in certain models - and you'll be up to your eyeballs in resources to help you counsel in just about every crazy situation you can imagine.
But you WON'T have good resources readily available to you to provide solid theology, biblical study, or history (for perspective).
Almost to the man I could identify those chaplains who had done a good "old fashioned" MDiv that focused on the languages, Bible, theology, history, etc., - regardless of denominational background - because their sermons and studies were simply better: more substantive, better presented, etc.
So my advice: focus on the most intensive MDiv you can find - so that *your mind* is prepared to do hard work, and then you'll be able to take that trained mind and apply it to hard things such as relational situations and all their complexities, interpreting command guidance, even dealing with base contracting office.... and oh, yeah, you'll be better prepared to be a real pastor to your flock.