Waterjet is trickey with composites. I have see problems with piercing laminate composites because before the jet makes it all the way through the part, some of the stream is diverted along the layers of the laminate causing delamination. You will likely get good results if you do not need to pierce the parts or have a pilot hole to start in.
Are your parts a honeycomb composite, foam core, solid 40mm <ouch>?
Find a good waterjet shop and send him some samples of your stock, he should (if he wants the job bad enough) do a test cut for you and then you can aprove the cut quality yourself. Test cuts allow for a more accurate price quote as well, especially in unknown material types.
I used to do contract work for the local waterjet guy here,
, send him a few pieces (1'x2' or so), describe the type of cut you are looking for (Square, Round, Different shapes, Tapered holes, etc), specify the accuracy you need and see if you like the quality.
Wayne Soule
KS Design llc