First of all, all the churches were never closed, although a lot of them were. Religious practices were never disallowed, although they were strongly discouraged at best. There were semi-official plans of eradicating all religion, for what I know they were indeed abandoned some time during WW2. The authorities wanted to get more support of the population which, despite their best efforts, still had a significant percent of religious believers. It seems that most of those reopened churches were, in fact, reopened by the Germans, then the Soviets just let them be. Religious persecution (of varying degree), nevertheless, continued almost until the end of the Soviet Union.
As for the numbers and years, I found this chart (in Russian), I can't trace it's origin, but at least some numbers seem to match, so I made a quick and dirty translation into English (sorry, I barely know those church names even in Russian, but I hope it's still understandable). The lowest point on the chart isn't zero, it's somewhere around 600.