Iodine and folate (or lack thereof) are big issues is you don't take supplements.
Iodine used to be in our milk supply but it is not any longer. It is vital for brain development and can increase IQ by approx 5 points if you have an adequate supply.
Food does not give adequate amounts of folate or iodine in most cases.
The children of this generation have IQ points something like 20 points higher than our grandparents mainly because of better nutrition.
Vitamin D is another issue - alot of people are lacking in this particularly in winter.
I would think the lack of vitamins and minerals would be more damaging than the manufacturing processing myself, but that is just me.
Either way goodluck with it all.