Hi,
You can set alpha to 0 at data level for the plots where the value is zero and you dont want it to be shown on chart.
Refer this sample, http://jsfiddle.net/0e9uza4h/
And if you want to hide the complete series you can set alpha:0 at dataset level for that particular series.
Share your observations,let us know if that suits your requirement.
Thanks,
Navdeep Singh Othee