Just testing out KSRSS on 1.11.1 with 2.5x SD config - the 'black moon' issue is present on (as far as I can tell) all non-atmospheric bodies, and is gradual depending on altitude - this makes me think it could be a problem with the way the detail levels of the bodies are rendered, as it usually changes depending on distance from the body, which is what is changing over this altitude - and presumably the high-detail, low-altitude texture is not rendering properly for some reason.
Also, they don't go completely black, so it could be more lighting-related, as there is still a bit of ground which is lit; it is easy to see in the craters.
I also got this message in the log (which I assume is related to the issue) - when going to a lower altitude where the Moon is no longer visible (it happens with every planet and moon, but the atmospheric bodies don't go black)
[LOG 15:48:44.597] [OD] <--- ScaledSpaceDemand.UnloadTextures destroying KSRSS-Textures/PluginData/MoonColor.dds and KSRSS-Textures/PluginData/Moon_NRM.dds
From what I can tell it looks like a texture loading issue.