That there is 40% less incidence in flu vaccinated patients is established by observation, but is it due to flu vaccine by itself or factors which surrounds itself in people more prone to flu or who are medically more conscious? (edit: think of analysis of variance tests among identifiable medical & socioeconomic variables). If the researchers establish a positive link, wouldn't it be worthwhile to then suppose that amyloid plaques are somehow related to viral influenza replication - which by itself sounds a bit absurd (edit: Ok lot of good reference about infections around AD. I take this back, my bad)
The alternative hypothesis is worth thinking too: Are people more prone to Alzheimer's also more prone to catching flu.