Actually, Stuka's were never available in large numbers. At their height, approximately 380 were available in 1940. That became about 350 in 1941 (for all fronts) and steadily declined from then on. After initial enthusiasm, the Stuka panzerknacker was eventually only operated by 1 group (about 40 aircraft). While very effective in its tankbusting role, it was vulnerable to marauding Soviet fighters. If used in 1941, they would undoubtedly perform extremely well because tanks were less well armoured compared to 1943/1944 and the Soviet fighters would have a hard time with Luftwaffe fighters.
But it wouldn't have made a difference in 1941 as destroying enemy tanks was not what stopped the Wehrmacht.
In 1943, the Luftwaffe had less than 400 fighters left to cover the entire Eastern front. Any panzerknacker, be it Stuka 87 or Henschel 129, would be vulnerable to enemy fighters under conditions of air inferiority. They would wreak a terrible toll of massed tank formations until Soviet fighters appeared. Then the tables would turn.