I'll accept results from any country/period of time since this doesn't seem to be something that would be too affected by culture or historical context.
Even in today's world it is shown that not getting enough nutrition when young will hinder thinking skills later in life. Did this cause most commoners to be stupid ( at least compared to us)?
I'm not a historian, but a biologist, and if the mods will allow it, i'd like to offer a view from a biological perspective since I don't think the question can be answered from a historical perspective. The reason is: there's no way to quantify the level of 'stupidity' hundreds of years ago by reading historical accounts. To answer your question you first need to adress the assumption you make that malnutrition is associated with a decrease in intelligence. I think this is the question that needs be answered first. Do you have any sources on this yourself?
A well known study on this topic was performed by Stein et al in 1972 (1). They examined the effects of a famine in the Netherlands under German occupation in 1945. At the time the north of the Netherlands was still held by German forces, while the south of the country was already liberated. The north suffered from a terrible famine during the winter of 1945, while the south did not. Stein et al. examined the intelligence of 19 year old males born in period (so their mothers were malnourished while pregnant). Surprisingly they found no difference in cognitive ability with their southern peers. However, a follow up study performed in 2010 found that in their late fifties, the famine exposed showed reduced cognitive abilities compared to the non famine exposed (2). So it appears the effects of the famine on intelligence only became apparent later in live.
Please note, I have not done a very extensive literature study on the subject, so there could very well be other studies out there which do show a more pronounced effect of malnutrition on intelligence. And of course this study only deals with the aftermath of one event. Chronic malnutrition during childhood might have a more detrimental effect on intelligence.
The introduction of Iodized salt to the United States in 1924 gradually increased average IQ by about 15 points (one standard deviation) in naturally iodine deficient areas (like the Great Lakes Region), and 3.5 points elsewhere, according to http://www.nber.org/papers/w19233. Iodine deficiency causes hypothyroidism, which can lead to mental retardation, depression, and delays in development in children, and is an ongoing problem in the world. There's quite a wealth of information on this topic on the wikipedia pages for hypothyroidism and iodized salt, including many excellent sources.