Cyd, I believe the trick is naming the files and folders in a way that makes sense to you. And it doesn't have to be complicated. For example, pictures from my digital camera are named with the code from the camera - but those numbers keep the pics in chonological order and then I have year folders in 'My Pictures' and I have our wedding pictures in a separte folder. It doesn't take long to find anything, especially with thumbnails.
So you can use a naming convention similar for new files you scan. I'm not sure if my new scanner does it, but on my old scanner, if I didn't change the filename from the last scan, it would use the same name with a number after it. filename, filename1, filename2, etc. That's good when you have a bunch of stuff the same.
As for how they are stored, think about it this way: not too long ago, we used the small floppy disks. my new computer doesn't have a floppy drive, but my parents' computer still does and I COULD buy and external one for about $50. And for a long time the computers being sold had both floppy and cd-rom drives. So you could easily transfer data.
I'm pretty sure the trend will continue, when something becomes less popular it fades out and you'll be able to transfer the files over.