There's a lot of variation in LEDs... 3mm, 5mm, 10mm, domed top or flat top, viewing angle, brightness, clear material or diffused... As Randy said that one's either a flat-top or one that's been ground down. But even if you get another flat top, there's MAJOR differences in brightness and viewing angle out there. For lighting up buttons and such you really want a wide-angle LED (and preferably diffused) so the light doesn't just shoot out the top of the buttons. (And I think Randy sells some diffusion discs for buttons? Or did I get those someplace else?) For the joystick balltops they might be diffused enough on their own that the LED angle doesn't matter as much.
I think if you just replace the one LED you may find that it might not match your other joystick(s). You could try, but I would suggest getting several LEDs of the same style and replacing them all. LEDs are pretty cheap on ebay... yeah it's stuff from China, and the quality of chinese ebay electronics is pretty shaky, but I've gotten tons of LEDs from there and never had any real issues. Be sure to add the current-limiting resistor, usually 100-150 ohms is fine.