Despite the feasibility of the underlying file-system, you REALLY should NEVER store that many files in one directory. When it comes time to browse the contents of that directory, you'll quickly discover that there is a HUGE amount of lag while the OS tries to build the file listing and such. It really puts a significant amount of strain on the system.
Most tools out there that do any sort of "web archiving" will usually build a directory structure similar to the website's layout. Nearly all websites do not base all their contents off of the root directory... i.e. mydomain.com/document-1 ... they will have some logistics behind it all that split it up into several paths (for a variety of reasons) i.e. images go in mydomain.com/images and stuff about goldfish are in mydomain.com/goldfish/ etc...
There are several tools out there that can & will build this sort of directory structure for you. even wget has options to download an entire site. Personally, I've used "httrack" in the past, and it worked quite well. There are also command-line options for wget to download an entire site as well. Look at the -r (recursive) option. Just make sure you setup your domain list so you don't download links infinitely across multiple sites. Best do some reading-up on the wget man page.