B8 class 1 stainless steel bolts/studs have a minimum yield strength of 30,000 psi compared to a B7 alloy steel bolt with a yield strength of 105,000 psi. I have been involved in many RCA of gasket failures where the B8 bolts were simply unable to develop the necessary preload to seat the gasket. You mention particular problems with NPS 3 and 8 flanges- these are the most under-bolted class 150 flanges, and thus are more likely to cause gasket leakage problems due to low bolt load with B8 stainless bolts. Also, B8 bolts, because of their low yield stress, are easily (and routinely) yielded during installation or service, thus causing more problems during subsequent re-use.
My rules of thumb for using low strength stainless bolting:
1) Don't, if you don't have to for external corrosion reasons. If you must use stainless bolting, use class 2 strain hardened- but be prepared to pay the price ($$).
2) Select "low stress to seal" gaskets that can be seated with the bolt load available. Do the calculations- don't let a gasket vendor simply tell you that its a "low torque" gasket.
3) Do the calcs and determine the necessary assembly torque, and then use a torque wrench so you don't inadvertantly tighten the bolts above their yield strength. For example, a 1/2 x 13 B8 bolt, lubricated, will yield at less than 30 ft-lb. What are the chances that a mechanic will yield this bolt if not using as torque wrench? Answer- 100% chance
4) Don't re-use stainless steel bolts
Finally, if you're using stainless bolts because your gaskets leak corrosive product onto the bolts- correct the leaky gasket and go back to using high strength, less expensive alloy bolting (B7).