When I was debating the bolts/studs question for my "Unicorn" model, I opted to use bolts on all the through holes and studs and nuts on all the blind holes. The result "looks right," at least to me. Though I'm not sure, I think that was traditional practice.
These days I think bolts are being used in places where formerly studs might have been the choice. Maybe it's because bolts are easier to make now than they used to be???
Studs have a locating value as well, that bolts don't have. You can drop the mating part onto the studs and it will stay where it's supposed to be, instead of having to hold the part in place while you try to get a bolt started.