Upgrading from OS X 10.8.5 to Yosemite: Potential challenges
I can't directly answer your specific questions but I advise you to wait before upgrading. Right now version 10.0.1 is out and I still have a couple problems I never had on Mavericks (now imagine all issues you'll have coming from 10.8). 
But as far as I remember from upgrading to Mavericks a year ago, I didn't lose any software or packages nor did I have any problems.