story
However, the flip side of this is that more freedom is not always good for more readable software. GOTO, for example, can express any control flow that for/while/do-while/if/switch can and a number that it cannot (coroutines/exceptions/etc.), but as an industry we've moved away from GOTO because most programmers can't hold this flow control in their heads. Prototypes are the same way: they grant a lot of freedom to implement fancy abstractions, but many programmers seem to be unable to understand the resulting abstractions, so they don't find widespread use.
Asking for codebases of 100K-1M lines in prototype-based languages is the wrong question. Because prototypes let people define abstractions that other programmers find unreadable, they a.) let you write equivalent software in fewer lines of code and b.) get rewritten in class-based languages as soon as you have more than a handful of programmers working on the codebase. They're much more likely to be used by a small team of hackers who sells their startup for $40M or so and then vests in peace while another team rewrites all their code in Java than by a big company.
If you broaden the question to "has anyone ever made significant money working on or with Self", the answer is yes:
http://merlintec.com/old-self-interest/msg01011.html
(Fun fact: Urs Hoelzle, Animorphic's CTO and sender of the second message in that thread, later went on to become employee #9 and the first executive hire at Google.)