How much reveal does the bottom edge of the facia have? In other words, how far down below the stucco does the lower edge of the facia hang? It wouldn't be a good idea to attempt hanging the board directly over the stucco, but if you have enough of the facia hanging down, you could install 3/4" furring strips fastened through the stucco and into the rafter tails and hang your beadboard to the furring strips. If not enough reveal from the bottom edge of the facia, the best approach would be to remove the stucco from the soffit. This would also give you a chance to install a continous run soffit venting if your attic space, (assuming you have attic space), needs more airflow. The cleanest approach to remove the stucco, ( messy but lessens the chance for damage), would be to cut the joint where the soffit meets the wall using a grinder with a diamond blade for masonry. Once that line is carefully cut, you can knock the stucco off the soffit with a hammer. You will want to cover any windows, doors, or anything else that needs protected with cardboard, tarps, plywood, etc to keep debris from damaging. Wear eye protection, gloves and a decent dust mask/respirator. The beadboard will probably need trimmed where it meets the wall after install.

What did you end up doing with the soffits? I’m in the same position