Just yesterday, Google started rolling out the second developer preview for Android M over the air, but also made the factory images available for those to flash. We're starting to see all kinds of new features being added as well as some being taken out, and others refined. One of those that was taken out was the dark system theme that was found in developer settings in the first preview.
It's important to remember that this is a developer preview, and not everything in there is going to make it into the stable release in the fall. And things are going to change, so the fact that this dark system theme was removed shouldn't be a huge surprise really. It wasn't actually ready for primetime, so Google pulled it from the second preview. Now because Google removed it from this developer preview, does not necessarily mean that it won't make a return this fall when Android M hits all Nexus devices - and gets an official name that starts with M. So it's not time to panic just yet, even though I think we'd all love to have a dark theme on stock Android, for those late nights that we are on our phones and the white colors are just too bright.
We'll likely see another update to the developer preview before Android M goes official this fall, so the dark system theme could make a return then after Google's engineers work on it a bit more. Having it adjust automatically for day and night though, would be a great feature to include in Android M, and it's something that a lot of apps actually already do on Android. Including Falcon Pro.
If you have the second developer preview, you'll definitely notice that it's missing from Developer Options, and there doesn't appear to be anything else that's new in the Developer Options area of the settings this time around. So continue testing your apps on Android M, so that when it drops in a few months, your apps will be fully compatible with Android M.