Hey, you really need to make up your mind on what you want to be.
All of the GUI is about easy access to things, which means users can avoid some of the complexity of the whole system. But if you really want to be a hacker/modder, then you are explicitly going for "outside" the provided-as-preinstalled stuff. You want more. Hey, that's fine. N900 is hackable and you will have the power to do that. But it means you have to deal with the complexity that comes from going over the border.
Even if the file manager would allow you to navigate the folders you want (it doesn't), you'd immediately hit another lack-of-functionality-bump in the GUI land. It just doesn't provide what hackers need. Never was meant to.
What you need is already there in plain sight. And that's called "X Terminal". Yes, it has more complexity than GUI. But it also has extreme power. Power that hackers and modders need. So just take a deep breath and dive, you'll be enjoying it immensively afterwards. Command line isn't such an impossible thing to learn, especially for hacker/modder types. Or if you are not willing to learn, then find a fellow hacker and ask him to write a GUI for you. But I'll tell you already that it's waste of everybody's time.