1. Can I use the Space Weapons Fix Mod with Autumn Twilight Mod?
No, that is not possible. The game only allows you to select one mod folder. If you want to use multiple mods, you'd need to combine them. However, those two mods are not compatible, because MarvinKosh and I have edited a lot of the same files.
2. Is it still worth installing LogicSequence High Res Mod? If so, has anyone tried to install it with the Ultimate Edition? I noticed the High Res Mod installer points to the Twilight folder but I'm not sure where to install it with the Ultimate Edition.
In my opinion, using the High Res Mod is worth it, because it improves the graphics a lot. I'm using the Ultimate Edition too, so that shouldn't cause any problems.
As for where to install the mod, placing it under Twilight\Mods is perfectly okay, as that is the default location (when selecting the Current Mod Directory in the game options, click on Default, and it select this folder). However, you could also place it under Galactic Civilizations II - Ultimate Edition\Mods, because that is the mod folder the game is set to when freshly installed.