If one does not pronounce the Shema correctly, one has not fulfilled their obligation (שולחן ערוך או"ח סימן סב). If so, then how could different pronunciations of the Hebrew words arise? Shouldn't at least the majority have heard it from their father, and on back, with exactly precision? Even if you would say that casual speech is affected by local languages, liturgical Hebrew is not casual speech.
Given this obligation to precision in pronunciation, how could variants in pronunciation have arisen, at least for fulfilling this mitzvah?