It is a bug and I've reported it here
http://aurora2.pentarch.org/index.php?topic=11945.msg144194#msg144194 in more detail. Essentially the routine that decides what kind of ship a ship is for the purpose of assigning a commander is a mix of "working in an unexpected way" and "definitely buggy".
In your case, the missile launchers are getting your ship classified as a military ship even though you're only using them to drop buoys. Arguably, the way the system
should be working is that if it sees survey sensors on a ship, it is a survey ship, full stop. Instead it is preferentially designating ships as military.
In the bug report I submitted this happens even when the only non-"survey" component is a
cargo hold, which to me smells like a bug. Hopefully Steve will check this out for 1.13.