The corrugated surfaces helped to save weight and drag, and they were readily available at the time. Today we would probably use sandwich panels for the same reasons, but 100 years ago those were not available.
Interestingly, the world's first all-metal airplane used already corrugated panels for the wing, while Junkers' first all-metal design was made from sheet steel. The aluminum panels for the wing and elevator of the Reissner-Ente were made in Junkers' factory and delivered to his colleague, Prof. Reissner, in 1912.
Reissner-Ente from 1912. Flying direction is to the right.
When the war broke out, Junkers felt he needed to contribute and started to build monoplanes with cantilever wings from 0.2mm steel sheets with corrugated panels welded below the smooth outer skin. The corrugated substructure worked much like the core in corrugated cardboard.
Junkers J-1 from 1915 (picture source)
Unsurprisingly, this lead to flyable, but very heavy aircraft. To lower the weight of his designs, Junkers reduced the skin to the corrugated panels and did away with the smooth skin on top, and he switched from steel to aluminum, a material which he initially avoided to reduce cost.
The low power of the engines of that time demanded low wing loadings, and surface friction was a minor contribution to the overall drag of aircraft of this time. Junkers monoplanes were the fastest fighters around, since they had no bracing wires. An additional benefit in the war for independence of the Baltic states during 1919 was their robustness - the fast shifting front lines made solid hangars impossible, and wooden airplanes were unusable after rain, so on many days only Junkers airplanes could take to the air.
Junkers J-9 (picture by Threecharlie)
If Junkers had wanted to reduce drag more, he would had made the landing gear retractable. But that would had added weight, just like a smooth layer on top of the corrugated one, and would had increased induced drag and had made the aircraft more expensive. The best compromise was to leave the corrugated surface exposed.
By 1932, when the Ju-52 flew first, this technique was already past its prime: Engine performance, construction techniques and wing loading had improved to a point that the better solution was to rivet stiffeners on the inside of a load-carrying skin. Junkers airplanes were very innovative first, but once the company had found a good way of producing robust, low-cost aircraft, it stuck to what it knew. However, Junkers' concept of a steel or aluminum truss plus the corrugated skin was heavier than the smooth monocoque skin which we still use on today's airplanes, and once aerodynamic drag could be reduced to a point where the drag increase due to the larger wetted surface of the corrugated skin could not be overlooked, even Junkers switched over. The Ju-52 was the last (and most successful) of the traditional Junkers aircraft, and the next one, the Ju-86, used the more expensive, but lighter monocoque design. Note that it had a retractable landing gear, but kept the Junkers Doppelflügel (the offset flaps and ailerons).
Ju-86 airliner of South African Airways (picture by Etienne du Plessis / Flickr.com)