Can't find the post but someone said that the dynamic desktop did change while in dark mode, but it only cycled between the various nighttime photos. I don't have Mojave installed so I dunno for sure but maybe someone who does (who also has location services enabled) can verify based on star appearance or cloud formations whether the desktop background is changing subtly.
I would think Apple is going to have to make some sort of change before release though. Dark mode was the biggest touted feature during the keynote and so I would think most people are going to have it on. And they did talk enough about the dynamic desktop thing to the point where many users know about it. It's going to cause mass confusion if the two are completely incompatible with one another (and for no good reason). I would think they are already getting a lot of negative feedback on that decision.