Almost guaranteed they are supposed to be ash trays. Note the metal liner, possibly removable for emptying. Japanese arcades are some of the smokiest places you'll find on earth. You could of course also use them to hold coins if that's your fancy.
Never found a Japanese arcade that ran on anything but cash. All 50 yen and 100 yen. Never tokens or cards. That could have possibly changed in the past couple years since I was there, though.