This is a classic example of begging the question, as to answer whether pre-modern cultures who practiced intentional cranial deformation noticed its debilitating effects, we first must establish whether there were any debilitating effects.
Keep in mind that, just sticking to the Americas (though skull modification is found globally), there were cultures were cranial deformation was the norm, and yet these societies practiced agriculture, complex social stratification, and monumental architecture. In areas like the Maya region (Tiesler 1999) and the Andean region (Gerzsten 1993, Shijman 2005), prevalence of some form of cranial modification can approach 90%. Yet, these are regions with sophisticated cultural and material practices. So, archaeologically at least, there is no indication to suggest cognitive deficits from intentional cranial deformation.
As skull shaping is no longer a widely practiced custom, anthropometry of human remains have been used to try and assess for potential physical and neurological changes. Tiesler (2013) on what is the most comprehensive examination of the subject, The Bioarchaeology of Artificial Cranial Modifications: New Approaches to Head Shaping and its Meanings in Pre-Columbian Mesoamerica and Beyond, essentially shrugs her shoulders on whether we can posit neurological deficits as a result of cranial modification, instead pointing towards risk for tissue damage from potentially overtight head bindings resulting in tissue ischemia. Dean (1995) looked at endocasts showing some narrowing of vasculature in deformed areas, but also found that cranial blood vessels compensated. Other studies have shown that various features of the skull and craniofacial morphology are altered, but that cranial volume is maintained (Gerszten 1993) and that even when we see features like flattened orbits leading to exophthalmasos, the overall orbital volume was unchanged (Nystrom et al. 2013), meaning there is no indication for seriously visual deficits.
Using craniosynostosis, a condition where infant skulls have prematurely fused cranial sutures, as a comparison is a popular approach, but there are problems with equating artificial cranial deformation with this condition. For one, the genetic mutations leading to premature suture closure can also lead to other malformations. Nystom et al. (2013) noted that one form of craniosynostosis can lead to temporal lobe malformations and overgrowth. Plagiocephaly, a general term for skull deformations, is another approach, but has many of the same problems. Miller and Clarren (2000) found about half of the individuals they examined for plagiocephaly had other congenital malformations or abnormalities, and that the biggest risk factor for developmental delay was prenatal stricture. In other words, it was compression of the skull during fetal development, rather than during the postnatal period which put children at risk for impairment.
So even if we see a higher incidence of cognitive disabilities in craniosynostosis and plagiocephaly, they are an imperfect comparison to healthy neonates undergoing cranial shaping. Indeed, even when studies have shown neurological problems in children with these conditions, the numbers are underwhelming. The Miller and Clarren study cited above did show a statistically significant use of Individual Education Plans for the patients studied as compared to their siblings, but the majority of subjects did not require any educational intervention (and the caveat about prenatal and genetic factors apply). Similarly, Speltz et al. (2005) found some slight difference in IQ and math abilities as compared to controls, but that the majority of asymptomatic craniosynostosis infants had no cognitive deficits. So even if we were to draw a direct comparison to craniosynostosis and plagiocephaly to artificial cranial deformation (a tenuous proposition) we would at best have to conclude only mild cognitive defects, and then only in a minority of those affects. Yet, this comparison is fraught with confounding problems of genetic and prenatal problems associated with other deficits and malformations. So, not really a good comparison.
In the end, we have no evidence of any sort of neurological deficiet from cranial modification in any of the populations that have been studied. Head shaping has been practiced in a wide array of places and times, without evidence that it adversely affected to the populations engaging in the practice.
Dean 1995 Sinus and meningeal vessel pattern changes induced by artificial cranial deformation: A pilot study International Journal of Osteoarchaeology 5(1)
Gerszten 1993 An investigation into the practice of cranial deformation among the Pre-Columbian peoples of northern Chile International Journal of Osteoarchaeology 3(2)
Miller and Clarren 2000 Long-Term Developmental Outcomes in Patients with Deformational Plagiocephaly Pediatrics 105(2)
Nystrom et al. 2013 Shape and Volume of Craniofacial Cavities in Intentional Skull Deformations American Journal of Physical Anthropology 151(1)
Schijman 2005 Artificial cranial deformation in newborns in the Pre-Columbian Andes Child’s Nervous System 21(11)
Speltz et al. 2005 Intellectual and Academic Functioning of School-Age Children With Single-Suture Craniosynostosis Pediatrics 135(3)
Tiesler 1999 Head shaping and dental decoration among the ancient Maya: archeological and cultural aspects. Annual Meeting Of the Society of American Archaeology 64
Tiesler 2013 The Bioarchaeology of Artificial Cranial Modifications: New Approaches to Head Shaping and its Meanings in Pre-Columbian Mesoamerica and Beyond