It just means that some idiot in their infinite wisdom created a interface and gave it a number and called it v3.01 to either accidently or intentionally confuse people, but added the rest so that he couldn't be accused of lying. A lot of people confuse this as meaning it is Windows CE 3.0. It isn't, it is Windows CE 2.11.
Well, it's called v3 because it's a third generation H/PC device. The .01 means it's a 9000 build of H/PC Pro (SP1 integrated). The confusion comes about because they should have called it
Microsoft® Windows® CE 2.11, Handheld PC Professional Edition v3.01