Studs are used all the time. Stud-bolts are just another kind of bolt, like hex headed-bolts. Just make sure the ASTM spec you are using includes stud-bolts. A193 does but I have not checked the others. I'd venture that API is more concerned about the material than the configuration.
Just to make sure, stud bolt in shell/roof manhole is allowed for API Std 650? Because i can not find any clear statement that we can use either hex bolt or stud bolt while the figure shown in API std 650 is using hex bolt.
I would not hesitate to use stud-bolts for an API 650 shell or roof manway. Section 4.7 does not mention or restrict bolting to headed bolts. Flange bolting charts usually include both headed and stud bolt lengths. Just remember to order enough nuts!