Related fact: the term "case" dates back to the old printing presses where characters would be individual blocks or wood or metal and they were stored in draws. Capital letters were stored in the draw above non-capital letters -- hence why they are referred to as "upper case" and "lower case".
In terms of your general point, upper and lower case letters were originally different stylistic type-faces rather than "modes" of a letter in the same type-face. It wasn't until relatively recently in our writing history that the rules of capital letters became defined rather than a style choice and I'm certain they weren't thinking much about the problems that might cause with string matching on digital systems invented several hundred years later.
cool way to bloat your glyph set to double the size and introduce aesthetic and string matching problems.