I would vote that "You have a high IQ" is better, preferable, the correct usage.
IQ means "intelligence quotient", whose definition, according to dictionary.com is:
an intelligence test score that is obtained by dividing mental age, which reflects the age-graded level of performance as derived from population norms, by chronological age and multiplying by 100: a score of 100 thus indicates a performance at exactly the normal level for that age group.
A test score (or an indicator, a measurement of intelligence) is countable, and as such, using an article, as demonstrated, is appropriate.
When someone says "You have high IQ", I believe, they implicitly substitute "IQ" for "intelligence", which yields the sentence: "You have high intelligence". Intelligence is not countable, thus, the article gets omitted.
This however begs the question whether one should say "high intelligence" or should one seek something better.
Consulting dictionary.com about intelligence:
- capacity for learning, reasoning, understanding, and similar forms of mental activity; aptitude in grasping truths, relationships, facts, meanings, etc.
- manifestation of a high mental capacity: He writes with intelligence and wit.
- the faculty of understanding.
Out of these definitions, only few seem to go well with the adjective "high":
e.g. "high capacity for learning" is okay.
But since other — valid — definitions don't form a good companion with the adjective "high", I would suggest that "high intelligence" is not an optimal compound.
There would be better ways to express this, e.g. "you are intelligent", or "you are very intelligent". Or even, I seem to recall the phrase: "high degree of intelligence".
In conclusion, when the acronym IQ is being used, I vote for using it with an article.