If HAARP can control hurricanes, why do we have to deal with them at all? Wouldn't any shadow government secretly controlling the weather have a strong incentive to divert any dangerous weather away from the US? The loss of life is low enough in each hurricane that a few black ops soldiers would be far more cost effective for eliminating enemies. Show me a power hungry autocrat that is going to feel okay funding fema knowing they could have just kept those funds for other things by preventing those disasters.
Or even better, direct them at our enemies and countries we don't like. Why hasn't Cuba been ravaged by decades of severe hurricanes leaving the country in shambles? HAARP has been around long enough they could have destroyed dozens of enemies of the US.
It's not like anyone could stop the US. It has the most powerful military on earth, most of the world's nuclear weapons, veto power in the international organizations that matter, and provides defense for most of the western world. What is the shadow government waiting for?