Why did the Junkers Ju-52 have corrugated external surfaces?
It was largely a structural decision. The Ford Tri-Motor which was designed to mimic many things the Junkers plane designs included, including the corrugated metal. 


  ...all of which were constructed of aluminum alloy, which was corrugated for added stiffness, although the resulting drag reduced its overall performance.


Corrugated metal is common for roof panels and ironically, hangars, these days. You can find some info on the strength and flex properties of it when related to those topics. Here is an interesting thread on increased drag (and load) on corrugated roofs. 

As for the availability of the material vs sheet aluminum I would argue that it had little effect on the design choice. Keep in mind all corrugated aluminum starts out as sheet aluminum at some point in the line so its hard to say there is more than one or either material. On top of that it takes more corrugated material to cover a specific square area than flat sheet material which would drive the price up. At that time period in aviation a lot of experimenting was going on and anything that made a plane a bit stronger or a bit faster was considered quite an achievement. Keep in mind we are coming of the tails of the fabric plane era so a design like this would have seemed revolutionary. The Ju-52/3m (the one you have pictured) came out in 1932 (work began in '28), by that time other makers were already looking at and working on smooth aluminum body planes. There is of course a large social aspect to the availability of materials at this time in history especially in Germany. I will refrain form a full history lesson here but you can read up on Junkers history here and about the man him self Hugo Junkers here which include some of his political views and his involvement (and issues with) the Nazi party. His work in all metal designs is credited with inspiring many passenger planes in the post WW1 and WW2 eras of design.