I'm not liking this change, assuming it's true.
Several of the apps I use frequently are distributed as ZIP files.
a) Some applications release the stable version in a DMG, but distribute the nightly builds in a ZIP file.
b) Plenty of open source software or freeware is zipped rather than put in a DMG because it's simpler. Especially if the open source dev cross-compiles on Linux.
c) As stated earlier many update routines use a ZIP to transmit the update, because unpacking a ZIP is more efficient. No need to wait for a virtual disk to validate and mount before extracting the update.
You just have to move the .app bundle into another directory, if it is bundled with other files. If it is the only item in that ZIP archive, then this will not affect it. Basically, the mechanism just wants to make sure that nothing that is bundled with it could be compromised. Developers can use signed disk images to avoid this entirely.