During WWII did the bombers have a full set of gunners after the Germans stopped flying intercepts?

No. The Pointblank directive, the primary part of the modified Allied Combined Bomber Offensive, ordered that the Luftwaffe be destroyed wherever it was found in the lead up to the beginning of the liberation of France. The U.S. bombed by day; German aircraft assembly plants and subcontractors were the primary targets. The German aircraft that did choose to take off and contest the attacks were to be eliminated in attritional combat with the bombers and their escorts; the Americans could replace their losses, while the Germans could not. After a brief pause in raids in late 1943 because of the disastrous results of "Black Week" capped off by the second raid on Schweinfurt (8-14 October 1943; 146 B-17s lost outright), a reconsideration in strategy was combined with improvements in equipment. Airfields and aircraft sitting defenseless on the ground, particularly those in a broad area of northern France as the invasion date drew nearer, were to be strafed and bombed by escort fighters released from their legs and returning home. The success of this plan became evident after D-Day, when the Eighth Air Force ordered on 7 June 1944 that one waist gunner be eliminated from B-17 and B-24 crews. On 23 February 1945, the second waist gunner was ordered eliminated. When a target or target area was known to be particularly heavily defended or planes would be flying in positions in the formation known to be vulnerable to fighter attack, some groups or squadrons returned one or both waist gunners on a mission-by-mission basis. Other modifications to crews were also made in the interim. The Norden bombsight was a top-secret device, removed from planes after each mission which amounted to a partial disassembly rendering the device useless, and kept under armed guard in a special building. A thermite self-destruct charge to melt the innards of the device into a shapeless hunk of metal is often claimed to have been an accessory, but this has been proven to be false; bombardiers were ordered to destroy the device if possible by firing pistol shots into it at specified points. Eventually, only the lead aircraft in formations came to fly with Nordens. Trained bombardiers were also a valuable asset, and "toggliers," who were often not full-fledged bombardiers or just other crew members of the aircraft who came forward to occupy the bombardier's seat over the target, would merely flip the switches on the bombardier's panel to release the bombs when they saw the lead plane drop theirs.

Sources:

303rd Bombardment Group web site

Pardini, Alfred. The Legendary Secret Norden Bombsight. Atglen: Schiffer Publishing, 1999.

Singer, Richard. 388th Anthology Vol. I: Tales of the 388th Bombardment Group (H) 1942-45. Bloomington: iUniverse, 2001.