Because it’s too specialized technology. You can use the best EH in each of your components (component Cost x2), and never meet anyone who uses HPMs. This technology is useless against all other types of weapons. This way, you will just waste a lot of resources.
Armor and shields protect against all types of weapons (with one exception for each). EH protects against only one type of weapon. It is often more profitable and cheaper for you to install more shields than to use EH.
EH also does not guarantee protection of components. You might just get unlucky, and one HPM shot will destroy your expensive (and because of that, the only) long-range FC on your flagship.
It has too many flaws. So the lack of cost increase just gives you a reason to use EH more than in Size 0.1 sensors or low-tech components.