Just to clear up a misconception, Footnote (now Fold3) does not have "about half" of the Civil War pensions online, and probably won't in our lifetime! They began scanning only the widow's pensions, and only about the first 3,000 or so. Thus, since FamilySearch's contract with NARA was only to do the first 3,000 or so, they used to have on that database that it was "41% complete", or something like that. In reality, there are 1,280,000 widows' pensions files from the Civil War; and many, many more soldiers' pensions, minors' pensions, and dependent parents' pensions; none of which they are scanning at all at this time. I know this because I do onsite research at NARA.

Keep in mind that the subscription services are always going to exaggerate about what they have. They are not ever going to tell you what they don't have. In most cases, thorough research still needs to be done the old-fashioned way.

Happy hunting!