The Soviets did count shared claims, as illustrated below:
Pokryshkin - 53 individual / 6 shared
Rechkalov - 56/5
Gulayev - 57/3
Stepanenko - 33/8
Alelyukhin - 40/17
Borisov - 17/10
Korobov - 3/10
Interestingly Ivan Kozhedub didn't claim any shares in his amongst his 62 victories. A full breakdown of Soviet claims can be found here:
http://users.accesscomm.ca/magnusfamily/ww2urs.htm