A pet theory of mine is that they simply were out-competed. If these processes require chemical concentration 100X over timespan 100X to form de-novo, but a basic prokaryotic structure may only require concentration 1X over timespan 1X, that could make de-novo synthesis entirely unfavorable. Once those prokaryotic structures propagate enough, it could be reasonable that the conditions for de-novo genesis would no longer be routine enough that it would play an observable role today. This also helps make sense of why more complex organisms would form de-novo - they would be entropically more stable ("Filling a niche").