Yes, all chemists suspected atoms were real, but they were mostly careful not to claim to have evidence for it that they did not, in fact, have -- yet! Nobody but nobody was surprised when we turned out to really have atoms. It was all a relief, but it didn't change much about how chemistry was conducted. It made catalysis easier to understand, and ultimately DNA as a physical basis for life that made biologists generally very uneasy. Many had thought of themselves as studying something divine, and had to get used to being chemists.