Why wasn't sauerkraut used to combat scurvy?

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The problem was that during the 18th Century, they didn't know that scurvy was caused by lack of Vitamin C (mainly because they didn't know what vitamins were). Therefore, they didn't go looking for foods that were rich in Vitamin C to cure it. It should also be noted that there was no clear relationship between a food's acidity and its Vitamin C content.

Much of the credit for curing scurvy is given to James Lind, who published "a Treatise on the Scurvy" in 1753 (in three parts). Lind was a doctor whose initial experiments on the causes and cures of scury were performed on 12 men of the Salisbury. These experiments seemed to suggest that the cure was the use of fresh fruit and vegetables. He later continued his experiments and released later editions of his treatise while attached to the Royal Naval hospital at Haslar. The Royal Navy only appeared to accept his findings some forty years later and finally add a citrus ration to the ship's victuals in 1795.

However, it's not that clear cut. Credit for linking vegetables to curing scurvy should actually be given to a Dutch writer, Johannes Bachstrom (whose work Lind did reference in his Treatise), who had concluded that scurvy "is totally owing to a total abstinence from fresh vegetable food, and greens; which alone is the primary cause of the disease".

However, Lind complicated matters by later in his treatise seemingly dismissing Bachstrom's conclusion by stating that people could remain free from scury while eating few green vegetables. Lind also mentioned other possible cures in his writings, especially the idea that exposure to dry, fresh air would cure scurvy, which meant that his conclusions on the causes and cures were not clear. It was probably that lack of a clear conclusion that prevented his work being widely accepted and, in part, delayed the Royal Navy adding vitamin C (even if they didn't realise that was what they were doing) to the daily rations.

Once the link between health and a diet of fruit and vegetables was accepted, Naval captains were required to supply their men with these foods. The actual mix of fresh fruit and vegetables would vary depending on where that ship was in service. Citrus fruit, primarily lemons and limes, was the most common but this was supplemented by locally available foods, which did include sauerkraut on occasion. Also James Cook had carried sauerkraut on his voyages, even before the relationship of fresh food to scurvy was established. 

Sources:  
The Health of Seamen, ed. Christopher Lloyd, Naval Records Society vol 107, 1965  
James Lind and Scurvy: A revaluation, Michael Bartholomew, Journal of Maritime Research 4:1, 1-14, 2002  
Feeding Nelson's Navy, Janet MacDonald, Chatham, 2014

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