I'd like to add to nzaman's answer about the "primary fuel production facilities" being hardened.
Oil often gets pumped from an oil site to it's processing plant via a many-times-miles (or thousand miles) long pipe that is very vulnerable. Pipes burst on their own (Google that for dozens of articles spanning decades) and are generally above ground, so are visible from even the air. They also have pumping stations which are not hardened or even heavily guarded. This also goes into natural gas production, since it's not only a common byproduct of oil refinement, but it's also present at the well and often needs to be removed before the well can be safely tapped for oil.
Coal mines can catch fire and burn indefinitely, if they get out of control. Bombing a coal mine with the right combination of chemical and incendiary device, you could create a massively hot fire that's hard to extinguish while a separate reaction creates a massive amount of oxygen to perpetuate the fire beyond coal miners abilities to control.
Nuclear power plants are particularly well built to withstand a bomb blast, since they are typically designed to contain themselves from blowing up, but there's still a lot of damage that can be done to them to prevent them from coming online anytime soon after an attack. The cooling towers and electrical grid tie-in could be severely damaged to the point where it doesn't even matter if the plant went critical, it still wouldn't be able to either produce power at a safe rate without cooling or it couldn't push the power beyond it's own site.
Depending on the level of technology of the nuclear power plant, a hacker can plant a virus/worm that'll take control of machines that operate the facilities and cause the machines to destroy themselves. This relates specifically to centrifuges for separating nuclear material and is just one example of what could be done with the right resources and/or willingness.
Another thing that could happen is to take out a large power relay point, similar to what happened in New York in 2003 that ended up with a domino effect that blacked out several states and provinces. This was due to a bug in the system, but a hacker or a bomb could do the same thing, if the attached grid isn't prepared for something like that happening. Since then, I believe the US grid was upgraded to better handle a major outage like that, but countries with less maintained or older grids might still suffer from a similar problem.
There's currently a major problem in California with their aging power grid causing wildfires. A well placed explosive may be able to do considerable damage that would take more effort than can be easily fixed in short order.
Secondary fuel production facilities are just facilities that don't produce the large amount of power and fuel that the primaries do. Because they aren't as entrenched in a civilization's constant need for power sources, they aren't generally as large of facilities. Nor are they as well used as the primary sources. In fact, because they are secondary, they are often times more distributed, which in turn might be why they are the secondary system.
Hydroelectric plants need to be in or near a large river or body of water. That doesn't necessarily help a township that's essentially landlocked. Power transmission over long distance is expensive and decreases the power being transmitted, so a smaller community might want a closer and smaller power source. That said, a bomb to the dam or the power plant will decidedly take a long time to fix, since it's not critical to a larger city needing more resources for more people.
The same thing goes for a coal fired plant. Destroy the plant and it likely won't get rebuilt. There might be political, legal, and environmental reasons for it not getting rebuilt, but it still ends up with not being replaced quickly.
Even a biofuel plant could be destroyed and cause major problems in supply of fuels as well as rebuilding the plant. Because they can be complicated and are under high pressure with sometimes caustic materials, the whole plant would have to be inspected and re-certified even if a fraction of it was demolished.
In the end of all this, there's a lot of ways to take out basic infrastructure that can seriously damage the ability of a country/city/state/whatever to defend itself in a timely manner. As far as a "hard kill", if a power plant can't be repaired in even 1-2 years, as sometimes a major catastrophe such as a high yield bomb can do, the facility might be written off as a total loss, even if it could eventually be fixed or only a portion of the facility was damaged. It may come down to politics or even just money. "Do we spend \$100M to replace a coal fired power plant that we constantly get sued about, or do we spend $250M on something 10x better that won't get us in trouble with the EPA and tree huggers?"