I am just wondering this, since it would be quite nice to know.
A good question, and an offical answer from the devs would be best.
However, I’m going to take an educated guess: Yes and No
Steam is good about letting you import save games, as it maintains a similar file structure.
The question becomes: Will old version saves be compatible with newer versions.
I’m 99% sure that the release to Steam proper will coincide with a major version update to the game itself. This major update may make so many changes that old save files might not work…independent of steam’s involvement or not. Or they might work but be unstable.
To be brutally honest, I don’t believe it will be compatible. There are a lot of changes that are happening with this, including the ability to make mutli-plats and much more. Am I saying that the old saves may not be playable? Who knows? I’m not a developer but in the past with games like Sins of a Solar Empire: Rebellion or Civilization V, I couldn’t play older saves because of the massive updates to the game. However, those games are pretty advanced compared to GDT (Sorry Patrick! Still love the game!). I would just wait and see for yourself.