The Niners had great success running the ball from this formation at the end of the 1960 season and the start of the 1961 season. When the shotgun was unleashed on the Colts in 1960, the Niners had 119 yards rushing in a 30-22 win. 3 weeks later the Niners played the Colts again...the Colts had already seen the shotgun, yet lost again (34-10) while giving up 152 yards rushing to the Niners. Some other rushing totals compiled by the 49ers shotgun offense were 186, 112, 137, 178, 259 & 324.
The 31-0 loss to the Bears, aka 'what killed the shotgun', is interesting in a few different ways. The bread-and-butter of Hickey's shotgun was the HB or FB (JD Smith or CR Roberts) carrying the ball on a sweep, or the Kilmer/Waters QB either taking the snap and running around end or rolling out to pass and then keeping the ball. The Bears/Halas/Shaughnessy figured out the only way the shotgun could beat you was by running wide. The only player who could run up the middle was the QB, and with no lead blocker or TE that wasn't really going to be effective. Brodie was a good passer, but Kilmer and Waters were not going to beat you with their arm.
Instead of playing their base 4-3, the Bears put MLB Bill George as a MG over center, but the key element was the Bears also split their DEs wide and had them basically holding their ground and waiting for the sweep. Unable to run wide and without the threat of a running game, the passing of Brodie/Waters/Kilmer was greatly hindered. The Niners ended up with 132 total yards of offense on the day. The Bears evidently got enough of a pass rush from George and the DTs to allow the Bears' DE spy strategy to work. Hickey had been using the shotgun as his base offense, and after this game the shotgun became more of a change-of-pace thing.
In the rematch against the Bears, the Niners had 536 total yards of offense. Brodie was 11 of 19 for 322 yards (!) and 3 TDs. Neither Kilmer nor Waters made the scoresheet. The Niners won 41-31. Perhaps this illustrates the limitations of Hickey's shotgun...but I am surprised that apparently none of the spread concepts of the shotgun survived. It seemed to be an effective offense for the most part.