You are certainly correct, Medal of Honor award certificates are indeed more rare than the medal itself. The certificates get lost, torn and otherwise become unavailable. Of course this is true for most award certificates, not just the MOH.

The certificate that the article pictures is not an original certificate. First, I must say that I do not know for sure that certificates were awarded during the Civil War, but I was sure that the text of the certificate that you illustrated was not such. I did not know the Medal of Honor Legion text so I looked that up. The legion was not formed until ca. 1890 so the certificate could not have been issued with the medal.

Interestingly, the legion was created in part to promote and honor legitimate holders of the Medal of Honor. That is a mission similar to the recently found unconstitutional Stolen Valor Act.

Here is an example of a pre-printed form letter which was sent with the Civil War MOHs. Note the hand stamp which reads, in part, BOUNTY PAID $1.00 1867. It was signed by the Assistant Adjutant General, War Department.

I don't have the same take on that Medal of Honor certificate as Fred does. This from the Medal of Honor Society web page:

"680 of the eventual 1520 total Medals awarded for Civil War actions (not counting those of the 27th Maine), have been presented. From 1866 to 1890 a total of 105 more will be awarded. From 1890 to 1899 more Medals will be awarded for Civil War action than were awarded during the war...a total of 683 in the last decade of the century."

This means that all (or at least some) of those MOH certificates awarded in the last decade of the century could be "original". This is especially probable, since I have been told, and I believe, that certificates were not issued with the medals before the Medal of Honor Legion was formed in 1890. It was sometime later that the individual military services started to issue certificates with medals. I have seen letters (but not certificates) sent with medals to next of kin for posthumous Civil War era awards.