Question
1.The home we purchased has a blue spruce tree planted next to the fence.  
One side of the fence is on the top of a retaining wall that is approximately 6
feet high.  Will the root system affect the retaining wall?  The tree is already
about 12 feet tall.

2.  we have another blue spruce that was planted about 5 feet from the
house. Will the root system have any affect on our foundation.  We have been
pruning it back every year to keep the root system small.  It is approx. 9 feet
tall also

Answer
No there will be NO problem with the roots from the blue spruce. At maturity the tree will have a spread of about 15 feet and the roots will spread out  about the same. They have a tap root going straight down and feeder roots out from the trunk in the first 2 feet of soil. These feeder roots will cause no problem and I would think this tree is a slow grower thee and it will be along time before the tree reaches mature size. Since the tree is near the  fence you may have to prune it as it get into the fence. This pruning will keep it small also.

The main problem with the tree near the house will be the branches rubbing on the house, Pruning will take care of this.