After a table is ingested to a target, is it possible to re-ingest only a subset of columns or un-exclude additional source columns without re-ingesting the entire table?

Once a table is ingested, the schema for that table is locked for any modifications. You cannot exclude columns as the downstream artefacts like pipelines and transformations might be dependent on this ingested table and will be impacted.

This is according to the design behaviour of Infoworks. You could always truncate the table and then make the modifications like excluding any columns.