EMP's affect electronics whether they are on or off. For example, your car is off, EMP Blast, your car will not start again. Your car is on, EMP Blast, your car will shut off and never start again. Batteries will also be toast. Don't know about fiber optics, but there is a link in the fiber optic chain that is electronic, so....
How to prevent? Make yourself a faraday cage, put what you want protected in the faraday cage, and it will work after an EMP. Google it for more info. You can make a faraday cage out of anything metal actually, garbage can, tool box, etc.
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