No the Mac Mini does not come with a install disc. It is like many OEM computers now and has a built in recovery partition that when you hold Command+R on boot will launch allowing you to restore the MacOS.
You can also create a bootable USB drive that does everything to recover your mac by download OSX from Apples servers.
As for 3D I am not sure but I dont think so. Last I heard anything about this it was requiring HDMI 1.4a spec for 3D output but the Mac Mini only had 1.4
The i5 version is only a dual core. You need the i7 for quad core. The mac mini does not come with any cables for monitors, monitor cables are normally only given with monitors not with the computer itself. It does come with a HDMI to DVI connector though to connect to any DVI monitor cable you may already have.
Yes, but it wasnt just the 2012 model many 2011 model users got the bug as well. The bug itself was in OSX Mountain Lion and was then fixed with I think it was 10.8.4. But now they are on Mavericks 10.9.1 so the issue is in the past now.