I had to go into the sound settings and select the correct output device again and it's been working correctly since. It defaulted to internal speakers and I re-selected line-out.
I noticed this as well... I've installed 10.10 on my Mac Mini and noticed it was not chiming. However the other day I reset PRAM on it (troubleshooting another problem), and as you may know, when you reset PRAM it reboots again immediately... the chime occurred on that reboot but then after Yosemite loaded, it was gone again on subsequent reboots.
I have Yosemite on my MacBook and I didn't think about this until you mention it, but now that I'm thinking back, I can't remember hearing a startup chime from it in a while...