I don't know about the specific example of Masters of Orion (could never get into those games), but I'd say that an older game CAN be worth less as time goes on, sensibilities change, and certain mechanics, control schemes or design choices are introduced that are then just expected to be in every game to the point where playing an older game then feels like a chore. So that would literally make a game be worth less as time went on.

Personally for me in these sort of situations, the greater moral outrage and queasiness comes from paying a company for a game at gog where that company not only didn't develop the game and just purchased the rights to it, but in cases like with EA and Westwood, actually destroyed the company that made the game I love and is profiting off the games they made.

But yeah, other than that, I don't REALLY have an issue with gog fixing up a game with dosbox and selling the convenience of playing it without too much hassle.