Will a FUE hair transplant affect the color of the SMP dots on our scalp?

FUE will not affect SMP.  If you are considering FUE and SMP it is best to speak to a doctor who specialize in both.

After a 6 months time frame there is no reason to feel the FUE hair transplant would affect the scalp pigmentation. Blending the two treatment though will require planning to ensure you create a natural look of hair density. Otherwise it may look patchy. It can depend on whether the areas still have existing hair or need to be dense packed. Also what you plan to do with your new hair when fully grown out. Whether you intend to keep the hair shaved still or longer. 

I do not feel that the color of the SMP dots will change significantly or become patchy if you choose to do some FUE graft placement in the SMP area.  I am doing more SMP and FUE combinations and have not seen any change in the dot characteristics.  Since you are 6 months out from the SMP and the dots are now stable, I think that you are fine to complete the FUE for enhancement.