No, Sahara hasn't changed.
Autumn was removed because of balance issues. We believe it too be underpowered - that's the 1st, and the 2nd - it will be back in Post-War Era mod. As of this moment, Valiant-class super cruiser replaced Autumn as a new mainstray heavy capital ship for direct engagements.
The issue is related to the recent base Sins update; it changed the way the rendering engine works, and added a lot of functionality related to loading mesh normals with higher resolution details, etc.
Unfortunately a few of the ships look less than stellar now, and are going to eventually need to be redone - which I must note, is being done currently. I'm not sure what the plan for the Sahara is, but it's likely to get a facelift in the future, that will clear up the issue in the recent releases.