The current German citizenry don't dictate the ongoing activities of the German government, and after WWII they had no choice, so their permission isn't necessary.

The Cold War-era West German clandestine/covert operations was run almost entirely by Western powers, particularly the US. The relationships between the German intelligence community (BND) and the American intelligence community (NSA/CIA) is still very tight, so that explains the nature of their relationship.

Many still harbor feelings that the Cold War may have ended, but the need (for the intelligence infrastructure surrounding it) never went away.