Spotlight peeks inside files to create an index, and Version-supported apps maintain a changelog of file diffs. These OS X features save data in hidden locations, separate from the file.
This means that:
(a) it is very difficult to delete a file and be certain it's really gone,
(b) you can't have a public area, a private area, and a highly confidential area on the same system; it's all commingled to the same level of privacy,
(c) you can't make a backup of the non-confidential files without risk of getting the confidential files too,
(d) pieces of an encrypted file (if you use TrueCrypt for example) might get saved unencrypted in Spotlight's and Version's hidden locations,
I could go on, but you get the idea. It breaks down the notion of a file having a distinct level of security or privacy, and doesn't replace it with a better notion.
We already had the following problems:
(1) deleting a file doesn't really remove it on any major OS, including OS X, unless you use a special shredding program, and these days even shredding may be ineffective on solid-state drives because of wear-leveling and caching,
(2) the swap space can contain pieces of a file,
(3) temporary files created by editors, word processors, and other apps might retain parts of file.
Now Spotlight and Versions make the problem even worse for Mac users who care strongly about privacy and security.
We're getting to the point--or probably well past the point--where you have to maintain at least 2 or 3 separate systems: one for public work, another for personal or private work, and a third for highly confidential work.