Font Book displays zero fonts

Reinstall macOS.

This might have something to do with me trying to remove the font cache following this guide https://gist.github.com/jaredhowland/2da83f0cc0fbb1ac523f

Perhaps, but that's probably ill-advised. A Safe Boot removes certain font caches maintained by macOS. That's all one should ever do.

How to use safe mode on your Mac - Apple Support

RWSupport58 wrote:

Reinstalling macOS shouldn't remove any data, right?

Right. In other words it's nondestructive, but it's good to be cautious. Sometimes (hopefully rarely) a Mac will fail catastrophically for reasons that can't be correlated to anything you might have done. As long as you have a Time Machine backup that prospect, however remote it might be, should never concern you.

Also, assuming I manage to go through all this, would I still have to safe boot to remove font cache, or would the entire reinstalling macOS process do so in the process?

I don't know if reinstalling macOS also performs the functions of a safe boot. Apple used to have a Support document that described what it does in greater, if somewhat cursory detail, but they no longer provide that information. An older version of that document contained the following (excerpt):

What is "Safe Mode"?

Safe Mode (sometimes called Safe Boot) is a way to start up your Mac so that it performs certain checks, and prevents some software from automatically loading or opening.

Starting up in Safe Mode does several things:

• It verifies your startup disk, and attempts to repair directory issues if needed.
• Only required kernel extensions are loaded.
• All user installed fonts are disabled while you are in Safe Mode.

Note: disabled, not removed. They will remain available after restarting your Mac normally.

Continuing that excerpt:

• Startup Items and Login Items are not opened during startup and login on OS X v10.4 or later.
• In OS X 10.4 and later, font caches that are stored in /Library/Caches/com.apple.ATS/uid/ are moved to the Trash (where uid is a user ID number).
• In OS X v10.3.9 or earlier, Safe Mode opens only Apple-installed startup items. These items are usually located in /Library/StartupItems. These items are different from user-selected account login items.

The boldface explains how Safe Boot handles font caches that might have become corrupted.

Just be advised that Support document has been removed and not simply "archived", and its information should be considered no longer valid.

Whatever files I found related to font cache (basically everything inside folders that had the words "font" and "cache" in them and were associated with Office) did not help after removing them.

You pretty much did what I would have done.

In the sprit of reinventing the wheel, Microsoft has always had its own way of handling fonts — the same fonts that are used with everything else the Mac does. As far as I know they're the only major developer who insists upon that, and it's a frequent cause of trouble.