If you check in the mod tab of the main menu option, if the checksum is 0, that means the game did not find any game files when you enabled the mod. Usually this is caused by a duplicate folder when you extracted the mod from its .zip file. You should have a bunch of files and folders in the folder for Sins of a Galactic Empire.

E.g. It should be Mods 1.85 -> Sins of a Galactic Empire -> lots of files folders like GameInfo, Entity.manifest. If all you see is a folder, you need to move all the files and folder up a level with cute/paste.

This is by far the most common cause of mods not actually changing anything.

For Armada 3, make sure you download the right version of the mod for your version of Rebellion. Make sure you follow any instructions on the mod download page as well.