If it's a question of SEO in maintaining that root position, what I would personally do is move the "root" documents to the new documents directory, and in IIS put in 301 redirects for each of those files that have moved. That way you have a roadmap toward consistency and don't have to maintain legacy file locations. Going forward the webmaster should use /documents exclusively.
Since it sounds like you're in the preliminary planning stages of your implementation, I'll give you another tip that would have helped us out when we were at that stage. Rather than using:
www.mysite.com/Data/Sites/1/documents/file.pdf
You may want to consider using:
www.mysite.com/Data/Sites/1/media/documents/file.pdf
The reason for this is that non-Admin users who are given access to upload files in the editors will be shown the file tree starting from Data/sites/[site]/media, so they wouldn't be able to see/replace files located in Data/sites/[site]/documents.
Because of this, we've recently been going through a major reconfiguration of our files to move everything under the media folders so we can begin decentralizing maintenance of our sites. Once we're finished with this reconfiguration, we will turn on the "ForceAdminsToUseMediaFolder" key in user.config so file access through the sites will be consistent for all site editors.
If I could go back in time, I would have turned on that key from the very start!
I hope that helps,
Jamie