Of course, this is guess from a priori reasoning. I would be genuinely interested if somebody tried file-based comments for a WordPress (or a similar platform) based site and it fell over or failed in some way.
The main reason you'd get failures in a flat file system would be the normal reasons you get a relational database in the first place. Either you get update anomalies, or you want to compact the data into single atoms, or you want ad hoc querying rather than a specific pattern of access set in advance.
It doesn't help that until 5.6 MySQL's query planner joined on disk if you tried to join any two tables in which one or both has a TEXT field, regardless of engine and regardless of the actual fields selected.
As you can imagine, this slows things down a bit, considering that's the core join performed for single post generation. It also makes every kind of "recent comments" plugin a performance nightmare (quite aside from their cache-busting power).
Wordpress divides posts + comments into 4 tables.
> which could be loaded asynchronously via Ajax for swift loading time and less load on the server (no slow view renders)
Wordpress can't assume any particular PHP + webserver configuration. Sometimes they're configured to send while rendering, sometimes the whole process blocks until it runs to completion. Ajax doesn't magically change that.
I also dislike the idea that I should need to download what is a small application to assemble a document ... when I could just download the document straight up.
When page loads get too long, I switch on pagination.
> cached with Nginx/Varnish, and further cached on the backend with Redis
My own setup is memcache for working objects. WP-supercache is configured to write gzip'd pages to disk and nginx is configured to serve .gz versions of page directly from disk whenever they're found. The OS file cache does the rest.
> I've seen WP sites that I had to debug/fix with 200+ queries per page.
When you see hundreds of queries per page, check your plugins and widgets. Wordpress is not my favourite software by any measure, but out of the box it's not that dumb.
Comments are non-negotiable features for many bloggers. 3rd party javascript is not the same in the eyes of many (including my little network).