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 Junker's first all-metal design was made from sheet steel. The aluminium panels for the wing and elevator of the Reissner-Ente were made in Junker's factory and delivered to his colleague, [Prof. Reissner][1], in 1912.

[![Reissner-Ente][2]][2]

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.

[![Junkers J-1][3]][3]

Junkers J-1 from 1915 (picture [source][4])

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 aluminium, 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 was their robustness - the fast shifting frontlines made solid hangars impossible, and wooden airplanes were unusable after rain, so on many days only Junkers airplanes could take to the air.

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.

  [1]: https://en.wikipedia.org/wiki/Hans_Reissner
  [2]: https://i.sstatic.net/ppMFl.jpg
  [3]: https://i.sstatic.net/HTUOU.jpg
  [4]: http://www.junkers.de/flugzeuge/flugzeugbau/flugzeuge_des_ersten_weltkrieges