There seems to be a plugin callback to resolve the link, which one can code to filter out web address, but that's beyond my league. The second way is to manual exclude ".url" from search with "-.url", or give a very low score to .url extensions so they appear at the bottom through pattern scoring, or -9999 to exclude it. The third way is to put all your shortcut urls in 1 folder and exclude the folder.
I believe the pattern scoring method should be the simplest.