This is a good question and I wonder why there isn't more discussion.

I generally fish herring in the Puget Sound and anchovies when I go to Canada (Nootka Sound specifically). Other places in Canada (Port Hardy) the preferred bait was plug cut herring. My guess is that certain baitfish are more common in certain areas and therefore used by the local fisherman. Puget Sound has herring populations so fisherman use herring. Ocean fish often feed on anchovies so anchovies are more commonly used along the West side of Vancouver Island. There is probably also a bit of local bias to choice of baits even in an alternative will work just as well.

My favorite way to rig a herring is plug cut....unless soft, then I will use a whole herring. For anchovies I always use a hood...either clear or green glow.