My personal view on this matter is that people in our industry believe high quality code means it's easy to read/understand. So assuming that the code is of good quality, the IDEs refactoring tools should suffice for navigating and understanding the code.

Now I admit for large projects (~ >50k loc), visualisation could prove to be very useful for architects or new people joining the room. But most visualisations tools are very text oriented, because of the underlying language itself. So what you end up with is the name of the class/package/variable in a rectangle with lines drawn to another class. From where I stand, that's very easy for me to either quickly draw on paper or imagine it in my head. So the tools I've come across don't add much value.

Another point which is only speculation is that a number of users are not visual, and have a different way of processing data. They'd rather read/hear about the details and numbers to "understand" what is happening, rather than visualise them.