Noticed there were some older questions regarding chart visibility/ Time-series visibility and workarounds.
Thought I would put my 2-cents in and throw what may be an obvious solution to some out there:
The previously answered solution regarding setting entire chart opacity to 0 to keep data ingesting is basically correct, no changes there.
However, I wanted to toggle the visibility of individual Time Series and you can achieve that by accessing and toggling Time Series disabled boolean.
From the smoothie.js source code:
   function TimeSeries(options) {
      this.options = Util.extend({}, TimeSeries.defaultOptions, options);
      this.disabled = false;
      this.clear();
    }
Example: 
    function toggleChnl(channel){
        if(channel.disabled == false){
            channel.disabled = true;
            console.log('turn invisible..');
        }
        else if(channel.disabled == true){
            channel.disabled = false;
            console.log('visible..');
        }
    }
Where channel = Time Series object (I call them channels for sensor streams in a system). 
Application applies to a common usage of creating a toggle based legend of lots of Time Series lines.