Can "at this late hour" be used to mean, "it's too late", even though it's not said in reference to time?
While it's possible, I think it still does imply some level of uncertainty as to whether "it's too late" or not. I suppose context would change it's meaning as well.
Michael Easter's quote, for example, does afford some uncertainty as to whether it's too late.
As far as my experience goes, I've mainly heard it used in either a situation of uncertainty, as above, or a situation where one does not want to do something "at this late hour".
One is suggesting it's too late "in the game" to do something, and the other is merely suggesting it's the wrong time to be doing something.
Yes. The phrase can be used with respect to a looming deadline.
For example, imagine an election scheduled in 2 weeks time: