This depends on the depth of the bed bug infestation and the makeup of your household. If you have small children in your home, remove anything that the child is likely to touch. Foggers are designed to propel the pesticides, so you should not need to move the shelves themselves unless you suspect there is a deep and large infestation.
Personally, I would cover the knick-knacks to protect them from chemicals which may damage them. The best advice is to read the directions carefully and follow them to the letter.