It's canon. For whatever reason, Vaders own life-support system is very vulnerable to Force Lightning.
Kind of makes sense, I suppose. If you were the Emperor and you wanted to keep your unruly apprentice in line, you're hardly going to protect him against your strongest attack, are you?
Actually Vader modifies his suit so that it is more resistant to force lightning. He knows it is a weakness and does as much as possible to mitigate it.
Palpatines force lightning was some of the strongest of any Sith lord. He is toying with luke but when Vader picks him up he amps it up to full blast, and Vader still throws him into the reactor.
If he was really vulnerable to force lightning he would have dropped the emperor and fallen down as soon as he was hit with it.