Java is not alone in this, turns out some conventions are great in large scale projects.
As such, code browsers always made this quite easy.
The fact that Eclipse provides a Smalltalk like code browser isn't an accident, rather its Visual Age roots.
It is only a problem when one makes the point to navigate through the source, outside Java tooling.
And using the JAVA ecosystem standard makes it easier for fellow/future developers to continue the support and expansion
There's room for a reasonable alternative that chops the directory structures into more reasonable nesting, for instance.