I still have some of the original versions of that joystick with my Atari 2600 and they definitely are not the most ergonomic of design and as Ian said they don't lend themselves well to long gameplay sessions.
Still it is a great idea, and having the built in feature to add more buttons is quite cool.
However I'm going to stick with my X-Arcade and Slik-Slik Classic controllers for most emulation. And my Atari to USB converter to use real Sega pads and Amiga sticks for authentic gameplay.
Most of the existing Atari joystick port to USB adapters such as the Stelladaptor, which can be used to connect a real Amiga joystick to your PC, are not easy to find these days. AtariAge doesn't seem to be selling it at the moment.
However I bought an Atari to USB adapter cable from a US company called RetroZone a couple of years ago and it works perfectly, even with multibuttoned joysticks. This adapter has the conversion circuit board built into the end of the cable with the Atari joystick port which you plug the Amiga joystick into. And so it looks just like a cable extension with a USB connector on the other end.
You can't buy the premade adapters any more, but Retrozone do still sell the kits to make your own. Take a look at http://www.retrousb.com/index.php?productID=125