How to remove shortcuts from Launchpad installed by Windows through Parallels 10?
Just found a useful article for my problem: http://kb.parallels.com/112798

1) Open finder, then press Shift+CMD+G and type "~/Applications/"
2) Locate your Virtual Machine's folder (there will be 2 similar folders, click on one that has application icons inside)
3) Remove all necessary shortcuts and they will be gone from Launchpad as well.