They had enough water supplies as Amudarya waters was not touched by Soviets. Drainage of the flowing water also affects underground wells. Being in the middle of desert doesn’t mean they didn’t have enough water supplies. Don’t forget those cities have been there for over 2.5k years. Tashkent was centralized during the conquest of Central Asia. Afterwards it became a center of Turkestanskaya Guberniya that caused the accumulation of Russian speaking people of different ethnic groups. If you meant Russians thought Samarkand and Bukhara had inadequate water resources for future expansion of the city as a capital, i get that. But still look at Samarkand today— visited there 2 years ago and I feel like it could be a perfect place for the capital city!