Apple has extended the sandboxing deadline again. There’s also a FAQ that states:
Apps on the Mac App Store prior to June 1 will remain on the Mac App Store.
We will allow bug fix updates to non-sandboxed apps that were offered on the Mac App Store prior to June 1.
This gives developers time to incorporate the new security-scoped bookmark APIs that were introduced in Mac OS X 10.7.3 (but not documented by Apple until a few days ago). The APIs make it possible to prompt the user once for access to each file/folder, rather than once-per-launch (with the original sandbox implementation) or not at all (pre-sandbox). There’s still the issue of these APIs being missing on Mac OS X 10.7.0 through 10.7.2, and there’s plenty more about the sandbox that still doesn’t work right. Nevertheless, this communication is a step in the right direction, and this time Apple didn’t wait until the day after the deadline had passed.
Update (2012-02-22): Daniel Jalkut describes the versioning issue. (I don’t think it’s as simple as the app checking the OS version, due to container migration.)