So I have a machine with four Intel Xeon E7-8895 v2. This is 60 real cores, but with hyperthreading enabled the system thinks it has 120 cores.

So when I'm evaluating load averages how do I factor in hyperthreading? Lets say my load average is 60, does that mean I'm at 50% processor utilization or 100%? I would presume that if the system thinks it has 120 cores then a load average of 120 would be 100% utilization. Am I correct?

It isn't easy to decide this. Very few programs can take advantage of almost unlimited cores. You'd almost never find a current OS and program running taking advantage of all of them equally. For most guesses, a modern OS with a modern compiled on latest program using full advantage of SMT will provide most level results.

The only way to tell if your use is faster with or without HT is to run some extensive tests.

At one time there were some serious bugs with HT but they are generally solved.

Some VM technology may affect how cores are used.

Not even close.
Have a good read of this.