I suspect a majority of the generic homonyms were created long before the Internet came along, back when it was more difficult to determine if a name was already in use in the literature. And the fact that there were two codes for nomenclature meant you didn’t have to consult the botanical literature if you were a zoologist, or vice versa. On those occasions when a zoological or botanical name was repeated, then the describer or someone else could come along and propose another.
The homonyms don’t bother me. They’re uncommon enough not to create a problem most of the time. Although once I did start reading an interesting paper about Gomphus (the dragonfly genus) before realizing it was actually about Gomphus (the moss).
Correction: Gomphus is a genus of fungi, not moss.