[latentsea]

Adding whitespace is a pretty simple solution. Heck if you really, really absolutely needed to resolve tonal ambiguity in kana you could add something to Kana to do that. That'd enhance the readability even further since, it's basically impossible for foreigners to learn correct intonation in Japanese unless they explicitly study it and that's on top of memorizing all that Kanji, but it would become explicit. I can recall exactly once in the last 10 years having a conversation where the there was ambiguity between two homonyms and someone asked a clarifying question to resolve it. The vast majority of the time it's just clear from context.

So.. I would say even that ambiguity isn't something people would actually have much a problem with.