Here is a USB 2.0 Isolator.

http://microcontrollershop.com/product_info.php?products_id=3769

I would recommend Saleae sale an add-on for this. I can see extra costs especially if you design this correctly. If you make all the channels isolated from each other (like a bunch of differential probes) that can be costly but may be necessary for some people.

I believe it should be very easy to plug in an add-on to the existing 100mil connectors of the pods.

Running it from a laptop does not solve the issue - if you are testing high voltage equipment (like an electric utility meter) and using an isolation transformer, the potential can be brought through the ground rail of the USB to the notebook casing... brushing against the "neutral" casing of the load on the meter and your notebook will give you a jolt. I speak from personal knowledge.

Why does someone not make a USB3 to optical to USB3 to isolate?

Just run it from a laptop! I'm doing that anyway because it is more convenient on my bench

External opto kit is the easiest solution.

Surge protection also important for instruments.
ESD (TVS), EMI/RFI (ferrit bead/ring) on USB.

There are USB optoisolators, maybe sell them separately.

Good feature, if any groups of inputs will be isolated individually. But I think it is too difficult and expensive to do that for analog channels.

You could try USB Isolator chip like this: http://www.ebay.com/itm/like/251485526057