At least in the HW1 missions (all I have played thus far). I built the research ship in the first mission as instructed, but noticed a few missions later that it does not show up in the fleet ‘Population’ rundown (shows 0 of 1 research ships). I double-checked, yes the research ship is still in the fleet and has not been destroyed.
I saw that as well when playing the Player vs CPU mode. It seems like it reports 0/1 until you have built the max number of research ship modules/ships (6 I think) and they have linked together to make “1” research ship.
I know this is an old thread, but it’s still a current issue. It’s not listed in the Known Issues page, so that’s why I bumped this.