I believe the best way to represent this table is as you have suggested: Using column 1 as a cell 5 heading and using three dots 5s to represent the blank entries. In table A, the repeated headings should make things clear enough.
In table B, you could put a transcriber's note as the column heading for the column that has no print heading: TNColumn 6TN. This would provide some extra clarity. Basically you would treat it as an embedded transcriber's note.
Cindi