I work in a large oil refinery with butterfly valves.  Our piping specifications are quite specific that piping flanges should be connected using studs, not bolts. The use of bolts would be considered a deviation from specifications and would require additional approval.  Studs are much, much more common as the preferred fastener in flanged joints in piping. 
With that said, the strength of these joints depends on the grade of stud that was used and the method of tightening it. If the specification called for Grade 8 bolts, then B-7 studs would normally be considered to be equivalent.  But, since the contractor cut up sections of all-thread rather than buying pre-cut studs which likely would have been stamped on the ends, it may be difficult to verify that the stud grade is correct. 
If you are responsible for the integrity of these joints, they you need to be sure that the fasteners are appropriate.  But, there is no fundamental reason that I am aware of that studs would be inferior to bolts as long as the strength was the same or better.   In fact, studs are likely to be superior because each nut can turn independently.  As long as they are tightened correctly, then you are less likely to have a problem with a stud.  I prefer studs and our specifications require them.

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