We have seen a disturbing uptick in incidents where structural work such as dormers, trusses, deck beams and the like have been attached with ordinary deck screws. It's simply not acceptable, and in some cases, can be downright dangerous, as screws have only a fraction of the load-bearing capacity of the nail required in such situations.
A notice from our building inspection department: wood screws are NOT suitable for any kind of structural framing.
Nailing table, here:
The prohibition on wood screws includes joist hangars: there are several brands of these available, and none of them accept standard wood screws as an attachment: the required number of nails (or engineered screws) must be used.
Engineered screws usually have either a Torx or hex head: these may be used for some structural connections.
If in doubt, nail it!