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Why wouldn't they?

Apple already sells Thunderbolt 3 to Thunderbolt 2 Adapter, so I am quite positive the Akitio Thunder2 would still work.

If I had one of these new Macbook Pros with me, I would test it right away.

Also, I believe there is Akitio Thunder3 available or at least in the works.
 
I'd say "probably". There are a couple of nice eGPU solution out already for TB3, like the Razer Core, Akitio and a couple of others. There might be some compatibility issues (I know for example that the Razer Core works great on some Windows laptops, but loses the connection or crashes a lot on other brands). The main downside, which doesn't have to be a problem, is that you can't get the output from the eGPU on the macbooks monitor. OS X doesn't support routing the picture back through the TB3 cable, so you'd have to connect an external monitor to the eGPU.. Although if you have a docking station with eGPU, I suspect most people would have an external monitor anyway.

Really interested in this solution as well, I'll wait until the mbp's are released and some people tested it, it shouldn't take long.. if it works well I'll re-evaluate the mbp's.
 
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