I just discovered the other day that you can basically just install a handful of coins onto a Ledger Nano S, even if it 'supports' hundreds.
Slightly off topic, but that's simply how many apps it can support at a time. You can freely delete and install apps without affecting your private keys or coins. I could install the bitcoin app, send bitcoin to the Ledger wallet, and then uninstall the bitcoin app to install something else, and when I later reinstall the bitcoin app a month or more later, my coins will show up just fine.
Isn't that an even bigger issue with linux?
Depends what programs you want to use. There are free and open source alternatives to the most common Windows packages, such as LibreOffice and GIMP. You can use Wine to run most Windows programs on a Linux machine. If you absolutely must use Windows for something, then you can always dual boot or have a separate Windows device.
I had no idea chrome was not recommended. Years ago I used firefox and then switched to chrome. I heard of Tor... but never used it because I don't know anything about it. I never even heard of Ublock origin. The only thing i heard of is adblock plus which is what I use with chrome.
So which is the best browser you recommend then? I heard of brave and microsoft edge. But make sure you use ublock origin with it? Is it better than adblock plus? The https everywhere and no script... i never heard of this. So these two programs would prevent any malware on the site you visit?
Here is your problem - you have no idea regarding what constitutes good security or good internet practices. I suggest you do a lot of reading. Chrome is terrible, Edge is terrible, Brave is terrible. No, HTTPS and NoScript aren't some magical shield which will prevent any and all malware from accessing your computer. Such a thing does not exist, and the fact that you keep asking for one piece of software to keep you completely 100% safe just goes to show that you don't really understand computer security.
Again, the windows scan detected tons of threats when I did a scan right after I clicked on the link.
It is incredibly unlikely that clicking on a single link has result in "tons of threats" on your machine. As I said above, your security practices are so poor that I suspect you have been infected with multiple pieces of malware for a period of time and you have just been unaware until now.
Move anything you can to your Ledger, and any coin/token so small and unknown that you can't store it on your Ledger then find a separate device which you don't go clicking random links on to download a software wallet to (or, you know, just sell it for bitcoin).