Why do so many huskies have heterochromia?

Very interesting question. It is obviously due to a evenly distribution of melanin between the two eyes.  In huskies it always includes one eye blue (1).

The reason is that this breed was developed by inbreeding together with the standards of the breed allowing blue eyes, and also heterochromia (for example malamute's standard is brown eyes, and heterochromia is not allowed), so the condition is not restricted by those standards.

Genetically, there are four ways of getting blue eyes in dogs, three of them related to the color of the coat causing white spots, patterns or diluted patterns, and only one that it is not linked to the coat. This last form is what huskies have and hence the color of the eye doesn't interefer with the normal pattern of the breed.
Breeders say that this is caused by a single gene, but i don't see they prove it in any way, because they don't tell wether it is a dominant character, codominant or recesive. So, i just tell what they say, but i don't give it entire credit.
This is the explanation given:

Lastly, blue eyes can be inherited as a completely separate gene,  unaffected by coat colour. This gene is, however, rare. It occurs  occasionally in the Border Collie and similar breeds, but mainly it's  seen in the Siberian Husky. Huskies can have one or both blue eyes, regardless of their main coat colour,  ranging in shade from almost white to sky blue. This is particularly striking when seen on black dogs.

Now, this only explains why do they inherit blue eyes independently of the pattern of the fur, but not why they have different eye color. And this last is very important, as they have the same genes in all their body, it seems that the development of the melanin is inhibited in one eye, and not in the other. This is not that strange (2). But what factor causes this inhibition is what remains unexplained, and I have found information regarding this issue.

Here is a good site about dog genetics:
Dog Coat Colour Genetics

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(1) Blue eyes are due to the Tyndall scattering of light in the eye, a phenomenon similar to that which accounts for the blueness of the sky called Rayleigh scattering. There are not blue pigments in the dogs eyes. Eye color is thus an instance of structural color and varies depending on the lighting conditions, especially for lighter-colored eyes.

(2) Heterochromia is very frequent in cats that have some form of albinism (there are various genes that lead to complete or partial inhibition of color in cats). This seems indicates that the "enviromental" factors opering during the development of both eyes are independent, although coat patterns tend to be very simmetrical.
I find this exciting to study the development of the fetus, and perhaps it could give us some ideas to understand some newborn defects such as cleft palates.
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As i told it is a very-very interesting quesion and I wish I knew more about this.