What changed in the Yosemite SmartCard handling?
Now I don't know the answer to your questions, honestly, it's something only Apple can address with proper justifications and references. But your impression is correct, they just don't care. Back in the day I used to use my government CAC to log in to my system (not for websites, that was my login method), it was hacky and took a lot of sudo commands to accomplish, but worked. That went away with Mountain Lion, and further more, sending an encrypted email with a smart card is torturous, something that should be a priority (personal security) above all else. Such a shame because I loved being able to do that as opposed to a traditional phrase passcode. However, I can still use my CAC for government computers, the same with Mavericks, with a 3rd party application. And this is not a sale, i don't know anyone from this company but it's just an example, just saying there are 3rd parties out there, but I ended up shuffling 30 bucks together just to get on my normal work websites. You can look into it pKard honestly though, you best solution and the more sane in the long run, install Windows with boot camp.

You can review their forums regarding your issue here but it seems like its a locally approved process for this particular software. I have not researched others.