This is going way way off topic. Question of TS was not whether or not to use Steam. Question was how it was possible that despite missions visible in the game directory, no missions could be found ingame.
I had the same issue. I believe that in 2.0 (openalpha) missions and campaigns are still work in progress.
However, if the missions are present in the game directory, you still can fly them, just by browsing ingame by pressing the little folder icon above the empty mission screen. If you browse to the correct directory, you see the missions appear.
DCS does that too. Just go to your profile and check serial. Or go ingame to module manager and press "serial number".
What snafup says. You even have it in the Windows Start menu: DCS Repair.