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Zero height markers are drawn with zero height. They can only be seen because all markers have an 1px border on barchart by default. Setting the linewidth to 0, a the bars with 0 height disappear: https://jsfiddle.net/simzer/x63umje8/2/
On the attached screenshot of an example, the first three rows have 0 (or empty) values in all years, but the markers still appear.
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