First off, are you familiar with the declassification of VENONA?

During that period, the Soviet relied on one-time pads to send ciphers. Given that WW2 demanded many more ciphers for military ops, the Soviets ended up having to recycle some pads. Once you start recycling crypto, it becomes crackable. By 1944, the early NSA and GCHQ were able to read about 50 percent of the Soviets' ciphers. When WW2 ended, so did the demand for ciphers, and the Soviets stopped recycling their crypto.

The thing is, the NSA and GCHQ captured so much data, they didn't finish decoding, translating and analyzing it until 1980. Also, most deep cover operations are long term projects with similar tradecraft, so those 3-4 years during WW2 ended up explaining quite a lot more than you'd expect.

The other thing though was that VENONA wasn't declassified until 1995, and it took several years after that for historians to really digest it. The fact of the matter was, that VENONA identified 300+ spies the Soviets were running in the West, and presumably many of those ran witting and un-witting subsources. Many supposed victims of the Red Scare ended up having more guilt that pop history really expected.

Ethel Rosenberg was once a poster-child for the supposed Red Scare witch-hunt. A mother with two young children, truly only a barbaric nation could execute her on guilt by association! There were massive protests to spare her. If you ever saw "The Atomic Cafe," they played a contemporary clip of a sympathetic witness to her execution. Well according to VENONA, it turns out she was guilty after all. Granted, their overall charges were trumped up, but they were indeed both Soviet spies.

Alger Hiss was another case worth mentioning. A fairly high profile figure with many powerful friends, he went all the way to his deathbed fighting allegations of Soviet spying. Quite a few in the media were conned by it. However, VENONA records point out an "ALES" who very much followed his pattern of life and access.

Another good example is the Cambridge Five, though admittedly the British side of the Cold War is outside my wheelhouse. Again, very prominent men with powerful friends spent their lives conning the media into believing they were victims. Again, VENONA pretty much sealed it that they were Soviet agents.

Though the other thing to keep in mind was the VENONA remained a very compartmentalized program. Originally an Army program, they actually hid it from President Truman because they didn't trust politicians, and even kept it from the CIA until 1952. Eisenhower was a general, so it became safe to trust the White House with SIGINT once he came to office. In fact, it's unclear where exactly McCarthy was getting his intel from, and I'm skeptical a mid-level politician would be trusted with VENONA.

VENONA also proved that the threat actually was out there. McCarthy fragged a lot of innocent people, but VENONA ended up proving that he was right at least some of the time too.