The layers are interesting but not overly needed for most when the vast majority of people could probably do everything they need on a 75% board without complaining about lack of keys - with the note that heavy number crunchers are going to need a numpad.
Most people are (a) n00bs and/or (b) stuck with cheap, more or less standardized commodity keyboards, MS Office and some defaults. The latter is forced by monopolies. Of course that requires high conformity.
I don't consider it relevant to the discussion, though.
Personally, I still have a heavy preference for entering numbers on the numpad. It's easier to fly through number entry that way. Not that I have to very often but it's nice to have when I need it.
The Model M's numpad isn't the only number layout out there, however.
It's okay in some ways, and in case of something like the aforementioned Kinesis Advantage (or even TypeMatrix), it can be easily embedded in the main section of the keyboard.
I, for one, prefer a (differently arranged) number row, that allows me to use both hands without jumping between rows.
There are other approaches too.
As for the Kinesis, the bracket keys end up down on the right-side arrow cluster area making their location more inconvenient than on Qwerty, Colemak, and even Dvorak layouts. If anything, the Ergodox offers a decent solution that symmetric keyboards create with the additional inner column per side. I've noticed some using the upper keys for the brackets in some instances.
Again, you're making assumptions based on default keymap/labels.
The brackets, for example, are placed in a corner or at an edge of the keyboard section, because they're rather uncommon: basically just arrays/parameters in some programming languages or tags in some markups. In either case, a good software environment at least automatically inserts closing brackets/tags, or better—abstracts away from "brute-force" typing (e.g., has a command/macro for making text bold).
Furthermore, keymaps (software or firmware) can be changed. On my keyboards, brackets/parenthesis are placed on a layer directly on the home row. I previously had them in the corners, middle (ErgoDox, wide-mod staggered layout) or bottom (Kinesis Advantage), but eventually stopped using those positions altogether, because of it required extra movements of the whole hand, or awkward stretching/curling fingers; I'm not a Tiproman (aka The Angry Chocolate Bar).