At first most customers insist of keeping the cabinet files inside the Windows Installer Database.
It may sound reasonable for the time being because you have to deal with lesser file count, but if you have a deeper look into the windows installer mechanics you will soon see some big disadvantages.
Its faster!
When deploying/installing/repairing a msi file/installation with multiple cab files it will be much faster than with only one file. Why? Its simple: Only the required cabinet files will be accessed and this results in less file i/o & less traffic (network share)
It will be cached from Windows 7 onwards
As many of you already may know microsoft introduced a new caching behaviour with Windows Installer 5.0.
Due to signing/certification issues cabinet files will no longer be stripped out before being placed into the Windows Installer Cache directory (C:WindowsInstaller).
This results in much more useless occupied disk space by Windows Installer Packages which are mostly cached anyway by the Deployment System.