Hierarchical namespace for uploaded files?

I'm in the process of moving an existing website to a new home, and at the same time converting it to Drupal (I'm using 5.6 now, but I expect to upgrade to 6.x in the near future). It's also my first actual use of Drupal for anything, so I have yet to find out how it works in reality.

The old website consists of about 100 files, nearly half of them HTML, but there are also images, PDF and RTF files, and a few other formats, neatly placed in a hierarchical directory structure reflecting their relationship to each other. As I move the site, the HTML files disappear into the node database, while the inline images and attachments end up in the files directory with its flat namespace, and the old hierarchy is gone. I have set the upload method to Public.

Fortunately, there are no name clashes among the existing filenames, so this particular move will not result in any immediate problems telling the files apart (for that matter, I haven't even tried to upload a new file with a conflicting name to see what happens). However, some filenames have now lost their context, and as the new site is expanded in the future, I expect it to contain a lot more uploaded files, so I want to find an intuitive way of naming them. A hierarchical directory structure would be intuitive to me, but if that isn't an option in Drupal, should I strive to mimic it using very long filenames (like newsletter-2008-2-cover.jpg for the lack of newsletter/2008/2/cover.jpg) instead, or is there some other solution?

Is it advisable for me to bypass Drupal and rearrange the contents of the files directory to my own liking, or would that break Drupal's internal book-keeping of those files (beyond forcing me to manually update every node referencing them)? Is there a file manager module that allows an administrator (or other role) to rename uploaded files in a controlled manner? Searching this site for "upload" documentation, I found a list of some 40 modules in the File management category, and I'm not even sure that's where I should begin looking for a solution. Maybe I'm seeing a problem where in reality there is none?

While I happen to be familiar with the GNU/Linux/Unix family of operating systems (since 1982, BSD 4), I want to let other editors help me maintain the site, and the actual semantics of mv existing-file-1 existing-file-2 is something I'd rather not have to explain to them, nor would I want them to use the webhost login password on a regular basis...