Portion of cost in GDP is not equal to importance.
What is the cost of water in the GDP? Much less than the cost of the energy. What would be the GDP without water? Nil. There would be no GDP because we would all be dead.
Water's cost is much less than the cost of energy because supply is high. If water was more scarce (or if water rights weren't screwy in many places), it would be much more expensive, and it definitely would be more of a limiter.
Also, you somehow equated the complete lack of a resource with a price increase. What would the effect on the GDP be without any energy? Well, we might not all be dead, but a significant portion of us might for various reasons including wars and massive world unrest because of instability. Even if you ignore all that, the economy as we know it would grind to a halt.
Considering that percentage is higher than margins in quite a few businesses I'd say it has a limiting effect on the economy.