This is odd, and I'm not quite sure why it happens. Someone has suggested me that you could move everything that comes inside Mods folder into Documents/My Games/Lucas' Simpsons Hit & Run Mod Launcher/Mods, maybe that could fix it.
If that doesn't fix it, please add my Discord Police Car#4790 so we could discuss it a little more in-depth.
Hey so I finally decided to bite the bullet and redownload the launcher. This has actually fixed the issues as far as I can tell - I'm nolonger getting missing hack notices, and have all of the mods on the list now to be selected/unselected. It must've been some stupid issue with the failed download somehow? I'm not sure. Either way, thank you so much for helping!