I always get nervous when doing an upgrade rather than clean install,
but the last two upgrades have been flawless.
backup or better yet clone your system drive first so you can revert
if there is a major problem.
I just updated 1 system same as yours (early 2009 tower) from mountain lion
to Yosemite. Everything works and no cuda issues. I did update to the latest
cuda and nvidia drivers too.
also did the latest yosemite 10.10.4 update.
my flip4mac plugin wouldn’t work but a free updated fixed that.
I’m running CC 2014.1