There's two ways I found.
1. Instead of making a shortcut to the LLB, make a shortcut to LabVIEW. Right-clik on the shortcut and choose Properties. In the Target Field, you should see the path to LabVIEW. After that, enter "
<Path to LLB>\
<Top Level VI>.vi". This will launch LabVIEW and tell it to open the VI inside the llb. So, for example, a user here posted a library recently. My shortcut Traget looks like "J:\Program Files\National Instruments\LabVIEW 8.5\LabVIEW.exe" "C:\NI pics\Keithley Data File\Keithley_DataFile.llb\Keithley_DataFile_migrated.vi"
2. Take your top level VI out of the llb. So you have
My Application.vi and
My Application.llb. Then you just create a shortcut to the VI.