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!

Hello again, you could try a reinstall if you feel like it might help.
Question though, have you taken everything out of legacy & put it inside Mods? I kind of admit I had a poor communication in there and didn't tell you to copy each file from legacy to Mods. Try doing that before reinstalling, might save you time!

I had extracted into the mods folder, and overwrote all the double-ups. When I had my issues downloading the launcher, the download had to restart a few times (chrome was not my ally that day). So I'm assuming it might've missed some stuff from that.

Some mods still work, being;
-Random Input
- No Peds
- No Audio
- Repair Car On Reset
- Speedometer
- No HUD
- No Traffic

Otherwise, I'm at a loss as to what's happening. I'm sorry if I'm not providing enough info, as I am very new to modding in any capacity. If there's any other info needed I'll be happy to provide.

Welcome!
Which version of the launcher are you using? The latest one should include all the latest hacks.
However, I believe some settings have been retired for some reason, so I have uploaded them for you here.
These should go in the Mods folder: Download

I am using the latest version for the Lucas Mod Launcher, being 1.26.1

I downloaded that legacy folder and put it into my mods folder, but it still has the exact same problems.
The exact wording I am getting on launch is "The 'Hack Support' hack is not loaded. Please make sure you correctly extracted all of the files".

After I click "Ok", it gives me the message explaining what mods aren't loading hacks. Do I need to try and reinstall the launcher or something? Because I had issues downloading the launcher file in the first place for some reason, and am wondering if I have to go through that again.

Thank you so much for your help so far.