She was just trying to be a smart-ass with that remark. The video of the incident shows she was being sarcastic. The tip-off to her ignorance came earlier, when the existance of her private server first came to light. When asked about her "unsecured" server, she explained that it was quite secure as it was on her NY property which itself was surounded by Secret Service officers.
Yes, there was evidence in spades that she was clueless, and it was throughout the campaign. I think of the number of people throughout out the working populations of the US, not even IT workers, who have routine familiarity with networks and computer nomenclature is huge, and it was that population that listened to Hillary’s ignorance, and said “not a good idea”.
The other message she was sending out broadly, but not fully recognizing the impact of, was the campaign slogan “Stronger Together”. This would typically be seen on the lectern she was speaking behind. Of course you also got to see her coughing bouts, and other signs of physical weakness, displayed with “Stronger Together” signs, and I think that created a low level dissonance that impacted many voters.