I have done several dome car rides in the past five years. You are asking the right questions! The conditions vary greatly among dome car owners and operators. In my experience, the cars that are (or recently were) Amtrak-certified private owner cars are generally good with respect to air conditioning and cleanliness. As far as tourist railroads on their own tracks, it depends on the size and reputation of the operation. The conditions on the Grand Canyon Railway for me four years ago were good with respect to comfort and visibility. (Not really that much to see or photograph from the train, however...) Mt. Hood RR last fall was a pleasant dome ride but the windows were filthy.
If you have a choice, the view from "conventional" dome cars, versus full-length dome cars, is superior. Budd single domes (e.g. California Zephyr, CB&Q, GN, NP) are my favorite! I always choose a dome car when it is available to me, whatever the price difference.