Andy, almost every joystick I own has a chrome shaft.
Wico balltops - Chrome (Most Atari titles, many conversion titles up to about 1992).
Happ supers mostly chrome. I am unsure about the current ones, but 5 of the 6 used ones I have owned had chrome, the other had chrome with a black plastic sleeve. (Many 90s games).
The Monroe joystick used a grey metal shaft that wasn't chrome. (Gyruss, Time Pilot, many other KONAMI pinout titles).
Original pac stick chrome.
Circa 1981 aftermarket Pac replacment stick chrome
Modern pac replacement chrome.
Data East style sticks - Black (Dedicated Robocop, Bad Dudes, and other games as well).
Every stick in every Sega game I have ever owned = Chrome (Clutch Hitter, Carnival cocktail, Space Firebird mini and the shifters on Turbo and Out Run).
Artic/ATW 4-Way = all black (looks a lot like an Atari 2600 stick, except hard plastic instead of soft). These don't hold up very well. They make a good stick if you just want to add a 4-way to your panel, but they quickly shatter microswitches if used as a primary stick.
Williams' 49-ways = Chrome.
Basically, out of the 15 cabinets I own, the 5 my neighbor owns, and the 20-30 I have owned over the years, I an only remember a couple joystick handles that were not chrome. And the ones that weren't also seemed to be the same ones that had a chintzy feel to them (Black handled super is the exception, feels the same as a normal one).
As for current cabinets. Newest joystick game I have seen on location (at least the newest one in a new cabinet) was an ultracade, and it had chrome handles.
Oh, and when I say chrome, I mean any shiny metal handle, as not all of them are actual chrome.