I don't use the data base values either, although I think that bolt weights are excluded. This would be the right way since you may be modelling a single flange, say on a nozzle or a flange pair in a line. If bolt weight were included then one of those would be wrong.
Beware that in higher pressure flanges, the bolt set can be half the weight of a flange, or more if over-length for tensioning equipment.