Bibliometrics in the social sciences, humanities and arts (SSHA) are hampered by the limited presence of scholarly journals in analysis tools traditionally used. We analyzed the level of indexing of Canadian journal author affiliations in Dimensions.ai and OpenAlex to assess effects on bibliometric research. Annually, around 3,000 articles signed by Canadian researchers and published in Canadian journals remained irretrievable. Incomplete indexing particularly affects journals associated with not-for-profit publishers and those publishing in French. A fair representation of national SSHA research could enhance our understanding of publishing trends and contribute to the sustainability of the Canadian journals.