[edited to reflect corrections in the comments]
It appears that shell came first, on the idea that if you were shelling something, you'd be more likely to be removing the shell than putting it on.
Though it's not found in the Oxford English Dictionary or Merriam-Webster, Dictionary.com does list de-shell as a related form to shell (transitive verb), and one can see by a search engine that deshell and de-shell are in some use.
I suspect that people use deshell because it reasonably fits the meaning of to remove the shell from – independently of shell (transitive verb), perhaps in environments where shell (transitive verb) is not used very frequently. Although at first glance it seems that they should be antonyms, by historical reasons they are used to mean the same thing.
From looking at the dictionaries, shell seems to have more prestige than deshell. By some loose Google searches, it appears that shell is more widely used than deshell.