Libraries like Guava and Commons don't have transitive dependencies - they are self contained except for other parts of the same library.
The same issue occurs whether you bundle all the code together or not, it's just that if you bundle it together you don't see what's happening and you can't use only part of it easily.
The same issue occurs whether you bundle all the code together or not, it's just that if you bundle it together you don't see what's happening and you can't use only part of it easily.