I won't shoot/hunt with anything but wood out of my selfbows....if I go to the trouble to build a primitive bow it just seems "defeatist" - is that a word?!- to use a high tech material shaft. Having said that, those carbons will shoot great from a selfbow. Being smaller diameter, they will lie closer to center on the bow, and should be quite easy to tune. They also, for the same smaller diameter reasons, and everything else being equal, should penetrate better.
If one is just starting out building selfbows, and is struggling with arrow flight - it happpens- and he/she finds that they can get good flight from a carbon, then I say "go for it". Hunting with primitive gear is a state of mind, and re-inforcing that ability, even in small steps, (using the bow, not yet the arrows) helps to develop that mindset. It doesn't have to be an all or nothing deal....ease into it, and keep your challenges fresh.
There are good ways to get more FOC in wood arrows, as well, so carbon is not the only shaft that is suitable for that. Woody weights are a great tool for getting weight up front....also internal footings are good.
If one uses the smaller diameter wood shafts (you should be able to find 5/16 shafts to fly from a 50lb bow) and weights the front and uses enough fletching to "correct" and steer, you should be able to get as good performance from your wood as you can from carbon.