I have a few Linux servers at home that I regularly remote into in order to manage, usually logged into KDE Plasma as root. Usually they just have several command line windows and a file manager open (I personally just find it more convenient to use the command line from a remote desktop instead of directly SSH-ing into the system), but if I have an issue, I've just been absentmindedly searching stuff up and trying to find solutions using the preinstalled Firefox instance from within the remote desktop itself, which would also be running as root.
I never even thought to install uBlock Origin on it or anything, but the servers are all configured to use a PiHole instance which blocks the vast majority of ads. However, I do also remember using the browser in my main server to figure out how to set up the PiHole instance in the first place, and that server also happens to be the most important one and is my main NAS.
I never went on any particularly shady websites, but I also don't remember exactly which websites I've been on as root, though I do seem to remember seeing ads during the initial pihole setup, because it didn't go very smoothly and I was searching up error messages trying to get it to work.
This is definitely on me, but it never crossed my mind until recently that it might be a bad idea to use a browser as root, and searching online everyone just states the general cybersecurity doctrine to never do it (which I'm now realizing I shouldn't have) but no one seems to be discussing how risky it actually is. Shouldn't Firefox be sandboxing every website and not allowing anything to access the base system? Between "just stop doing it" and "you have to reinstall the OS right now there's probably already a virus on there," how much danger do you suppose I'm in? I'm mainly worried about the security/privacy of my personal data I have stored on the servers. All my servers run Fedora KDE Spin and have Intel processors if that makes a difference?
I'm not going to judge you (too much), it's your system, but that's unnecessarily risky setup. You should never need to logon to root desktop like that, even for convenience reasons.
I hope this is done over VPN and that you have 2FA configured on the VPN endpoint? Please don't tell me it's just portforward directly to a VNC running on the servers or something similar because then you have bigger problems than just random 'oops'.
To be honest, you're most probably OK - malicious ad campaigns are normally not running 24/7 globally. Chances of you randomly tumbling into a malicious drive-by exploit are quite small (normally they redirect you to install fake addons/updates etc), but of course its hard to tell because you don't remember what sites you visited. Since most of this has gone through PiHole filters, I'd say there's even smaller chance to get insta-pwned.
But have a look at browser history on the affected root accounts, the sites along with timestamps should be there. You can also examine your system logs and correlate events to your browser history, look for weird login events or anything that doesn't look like "normal usage". You can set up some network monitoring stuff (like SecurityOnion) on your routers SPAN, if you're really paranoid and try to see if there's any anomalous connections when you're not using the system. You could also consider setting up ClamAV and doing a scan.
You're probably OK and that's just paranoia.
But... having mentioned paranoia... now you'll always have that nagging lack of trust in your system that won't go away. I can't speak to how you deal with that, because it's all about your own risk appetite and threat model.
Since these are home systems the potential monetary damage from downtime and re-install isn't huge, so personally I'd just take the hit and wipe/reinstall. I'd learn from my mistakes and build it all up again with better routines and hygiene. But that's what I'd do. You might choose to do something else and that might be OK too.
I have never accessed any of my servers from the internet and haven't even adjusted my router firewall settings to allow this. I kept wanting to but never got around to it.
Yeah this and other comments have convinced me to reinstall and start from scratch. Will be super annoying to set everything back up but I am indeed paranoid.