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Two elements can be araised to answer the question.
First, the Gulags of the tsars and of the Soviet Union were very different: different people were put there, and they had different conditions of life.
During the ImpΓ©rial period, some cities effectively develop from the families of people sent to Gulag, and with the other infrastructure around these prisonner camps. However during the Soviet period, Gulags were not developping in cities as the prisonners were moved from place to place to participate in different works. Also, a lot of people who were "gifted and freedom loving" were separated from each other, and sometimes executed, as a way to prevent uprising.
So how did the cities in Siberia developed? The major factor is World War Two: the massive movements of plants and industrial facilities to the East of the Uram began the de facto relocation of very skilled workers,that before the war ware working in industrial regions west of Moscow or in Ukrainia. These movements could have inverted after the war, but many land resources were discovered (gas, oil, coal, iron...) and thhese discoveries led to even more industries to be settled at the East of Ural and in Siberia.
Thus, those cities with massive engineers and tech workers population, from all social classes, were built. Living conditions are difficult, but as in other European countries, the technological middle of the workers led their sons and daughters to work also in technological industries.
Add to these situations the revolution of internet communication, that allows someone in Tomsk to have nearly the same possibilities as someone in the Silicon Valley (which was also at the start in the 90s a "background playground"), and you have the conditions to find Russian hackers in the middle of nowhere in Siberia.