On one hand, I think there is some historical truth to it. The gurus, from what I understand, as well as the Khalsa, were generally drawn from Aryan/Punjabi population, so I think it's fair to presume that they would have been inclined towards lighter complexions. The broad varieties of Sikh tonalities we see today are due largely to later spread of Sikh knowledge.
On the other hand, though, you're absolutely right that artistry shows its biases. Sikhs (and the Hindu artists behind a lot of Sikh paintings) fall prey to subtle prejudices and subconscious racism as anyone. As you said, 'virtuous' and 'saintly' subjects in Sikh art tend to have glowing white or pink complexions, while demons, executioners, thieves, Mughals, or whoever else is representing wickedness are almost unfailingly presented as dark-skinned. These are deeply-entrenched conceptions and things we Sikhs ought diligently to root out, as they fly in the face of righteousness and spiritual truth.
Forgive me for forgetting the specific story, but there is the incident told of how one of the Gurus was at a lakeside observing how, due to the holiness of the waters, black crows were entering the water and emerging as white doves. Give me a break. Tales like this don't exist without the deep-seated prejudices and fears people are prone to.
ਬਲਿ ਬਲਿ ਜਾਉ ਸਿਆਮ ਸੁੰਦਰ ਕਉ ਅਕਥ ਕਥਾ ਜਾ ਕੀ ਬਾਤ ਸੁਨੀ Ang 827