Do Famicom Disks actually have a filesystem like other magnetic disk media? If so, has it ever been cracked? If not, perhaps I could try to disassemble the Famicom Disk System firmware and crack it.
It does, and it has been. There are a few different tools to do this, and the source code for one on the NESDEV forums. The link: http://nesdev.parodius.com/bbs/viewtopic.php?t=3203
Well documented and the FDS Bios itself has been disassembled too. If you're interested search for Brad Taylor's FDS document.
I can't seem to get that to work for any of the FDS rips I have. They are No-Intro, so I'm 99% sure they are clean, but whatever. Still cool to see that research has been done into this =D
Orly? XD This would be more difficult and almost certainly less fruitful than you think. No-Intro are talentless ROM collector kiddies. There is nothing clean about the images, they are the same FwNES dumps from 13 years ago, just with manually erased save files at best. MAYBE one of them has a FDSLoadr, which is useless for archival because the FwNES format is flawed not being a literal copy of the disk. There are better programs for viewing disk structure than the one above, but not one end-all. This one is closer: http://nesdev.parodius.com/bbs/viewtopic.php?t=1355
Is it possible to dump disks and make a 1:1 image? As far as I knew, it wasn't possible with any publicly known method.
So it's "possible", not currently being done anywhere. I would like to dump a few white disks and my pink disk, but I'd like to only need to do it once, correctly.
Yes, nobody is dumping disks at the necessary level; the MGD comes close but it too drops data considered outside of a file. It attempts to detect this however and will modify the structure/add it's own flags to its images. If the MGD can, so can a CopyNES or just a controller-PC cable. In order to have one end-all dump it'd be best to bypass the RAM adapter like FDSLoadr, greatly oversample a pass of data, and then process the bitstream for errors. Since no one is running DOS for FDSLoadr it'll take new hardware.