Question about the aftermath of antivirus use and trojan virus

I read around the forums here that it can remove some important data from the system... Is this irreplaceable and permanent even after the antivirus is removed?

That is correct. Permanently damaged... no. For example you can always completely erase the affected Mac and reconfigure it from the ground up. That is an extreme solution, but it has been absolutely required for certain "anti-virus" products I am familiar with. The good news is that I do not believe Avira, Bitdefender or Norton are among them — bad though they may be.

Vulnerable to malware... possibly. Actively using "anti-virus" products will definitely increase a Mac's threat profile. Not using them is preferable, uninstalling them (in the rare occasion their uninstallation instructions actually work) even more so.

At the moment I'm on Sonoma 14.4.1. When a new update is available, can any missing system files be replaced again through that process?

... probably, but it gets complicated. More about that later.

2) Can trojans find its way into Mac and cause damage? Can it cause data breach?

Not really. First of all a Trojan isn't a virus (there are no macOS viruses) but it's something that you have to deliberately install — like "anti-virus" junk. Anything that asks for your login credentials needs to be taken seriously, because macOS won't ask for them otherwise. There are plenty of programs that are poorly written, others that are deliberately malicious, and some that are just plain garbage that serve no beneficial purpose.

Can using any one of those hypothetical programs directly result in a "data breach". The answer depends on how you choose to define those terms. Like any information-containing appliance, a Mac contains lots of data, and much of it is likely to be personal. If data exists on a Mac it can be harvested, uploaded, correlated, stored, distributed and sold, depending on how you decide to use your Mac and what you decide to install on it.

Is that a "breach"? You decide. Plenty of people willfully install programs on their Macs specifically designed for the purpose of collecting the information on them for any conceivable purpose — though they all have the same ultimate goal: 💰. "Anti-virus" products are certainly among them.

I don't have any issues at the moment, everything seems to be running smoothly, I'm just worried.

Then don't worry. Read Effective defenses against malware and other threats - Apple Community. Hopefully it will ease your mind.

For advanced study consider using EtreCheck: How to use the Add Text Feature When Posting Large Amounts of Text, i.e. an Etrecheck Report - Apple Community contains a brief description of what it is and how to use it. At your option you can post its report in a reply to this Discussion. If any "anti-virus" remnants are present on that Mac EtreCheck will readily identify them. They may be inert, or they may still be affecting that Mac to an unknown degree.

1. No.
2. Yes, theoretically. macOS has a number of security measures in place to help prevent this, but any device is vulnerable to viruses, malware, and spyware. You should practice good internet hygiene to help avoid getting infected: Protect your Mac from malware - Apple Support and Ways to avoid malware and harmful apps on Mac - Apple Support.
3. Those warnings were probably not related. Antivirus software is also extremely likely to flag things that may appear to be viruses as infected or dangerous when sometimes they are not. False detections are common, and may even be motivated by trying to keep you subscribed to their product.

I wouldn't worry too much about it if you haven't been downloading much beyond antivirus software. If you want to do a quick scan for free, try Malwarebytes: https://malwarebytes.com. It's a really great free option, so you might consider just leaving that installed and running to help ease your nerves. :) Try to avoid downloading things outside of the macOS App Store if you can, which will help keep things secure.