Yeah I had a similar feeling with Zen Cart recently, my mind was blown by just how many files were included in each page and the complex paths through which it happened, also the very high complexity search queries which perform terribly.

I think the issue is this software is more designed with allowing non programmers to get most of the way to a functioning website in mind rather than programmers. To someone with limited knowledge of what's under the hood they probably love the choice they get with modules and configurations abstracted away from the code.