However, when I load the mod I do not see the usual "ships" in the background of the menu
This is because we have changed out the menu map to one without ships, at least for now. We need to code in the "cosmetic" versions of the ships to use on that map; with the old version, you could hear the engines of the ships humming the whole time, and people were reporting it as an audio bug.
I would say maybe a medium setting in game despite me being set to ultra. I have tried lower graphics in various settings thinking it was my video card as well I have tried other mods for Sins with max settings and only Ascendancy seems to be affected.
You mean the mod looks worse now than it did before? If it looks the same, then it's not any sort of bug. Them improving the texture resolution of base game textures wouldn't make the mod's textures higher resolution. What they did was essentially add in LAA support to the game, and then took advantage of it for the base game assets. Mods already required LAA to begin with, so we don't get that much extra room to work with- if we were to try to make 4K textures, the mod would run into the stability issues mods with lots of content were running into without LAA.