Far bigger of a problem to me seems to be how many characters are pronounced the same. I suspect that the common usage of it avoids words that sound the same and cause confusion, but it is still a problem.
For example,
偒 was pronounced /*l̥ʰaːŋʔ/ and 陽 was pronounced /*laŋ/, but the modern pronunciations are tǎng (/tʰɑŋ²¹⁴/) and yáng (/jɑŋ³⁵/) respectively. So the phonetic part 昜 /*laŋ/ no longer consistently represents that sound, although in this case the final -aŋ is still present.
And as for sounds that were present in Old Chinese but not in Middle Chinese and Mandarin, like [2] 巽 was pronounced /*sqʰuːns/, now xùn (/ɕyn⁵¹/), they underwent a series of regular sound shifts that make them sound quite different when used in characters in Mandarin.
Also, Old Chinese was not a tonal language, tones first appeared in Middle Chinese, which the modern system derives from (with changes). Tones never had a chance to appear in writing.
[0] https://en.wikipedia.org/wiki/Chinese_character_classificati...
> I suspect that the common usage of it avoids words that sound the same and cause confusion
This problem is solved in modern Chinese by making most words more than one syllable long.