The orders were for separation, not destruction, but in many localities they were taken as licence for the latter. The movement known as haibutsu kishaku, abolish the Buddha and destroy Shakyamuni, saw temples closed, images broken or sold, sutra collections burned and bronze fittings melted down, with the losses varying enormously by domain according to the enthusiasm of local officials. A great deal of what is now regarded as Japanese cultural heritage was lost in a few years, and some of what survives in Western museums left the country in this period.
The deeper consequence is conceptual, and it is why this event matters to a reference work. Before 1868 there was no Shinto in the sense of a bounded religion with its own clergy, doctrine and institutions distinct from Buddhism. The category was produced by the separation, given an administrative structure, and then declared by the state not to be a religion at all but a body of national rites binding on everyone, which is the arrangement usually called State Shinto.
This is why historians of Japanese religion treat the word Shinto with such care when applied to earlier periods, and why the atlas records the modern category as the outcome of a policy rather than as the continuous name of an ancient faith. Kami worship is genuinely ancient. Shinto as a religion with a boundary is a modern construction.