MOST Amiga games certainly did NOT take advantage of a dual button joystick. MOST 2-button joys are actually wired to be one button - just in different positions. Usually one on the base and one up top.
Cammy is absolutely right on all counts, especially about lazy programmers.
Out of the boxes and boxes I have of just about every DB9 joystick ever made, only ONE of them is wired to be 2-buttoned. It's an extremely rare Epyx one too.
Funny thing is though the Sega Master System from the mid 80s had plenty of multi-button joysticks with the D9 connector.
And in a way companies like Competition Pro or Zipstick makers carried on using two buttons wired to the same pair of pins, which only let the problem fester.
It's a stark contrast to people like Sega who launched special 6 button joypads so people could play SF2 properly on their console. There was no reason why Commodore couldn't have made a joypad for the A1200/600 at the very least and have a quiet word with the big software companies.
I think the CD32 was a bad idea though, even the AGA chipset wasn't a match for the SNES custom chips and Commodore had no experience in this area of the market. Bad idea to make CD32 their last ditch effort, they should have stuck with the A1200 and upped the specs a bit with a small amount of Fast ram say 512kb. a HD floppy and 3.5" internal IDE HD for price reasons and finally a 28mhz clock doubled 020 which wouldn't have cost much at all. The system bus already runs at 28mhz and divisions of it hence 14mhz and 7mhz 1200/600.
Regardless of how technically good/bad things like Sinbad/King of Chicago and Defender of the Crown were, the point was Cinemaware in conjuction with Sachs were pouring their heart and soul into making the next generation of home games, and for that I loved them

Edit: Actually I think CU Amiga magazine published the source code for reading all the buttons on the standard Sega 3 button joypad on one of their cover disks. So clearly it was an issue with a simple enough solution.