It's linked via Homebrew, which you can use to install and keep some .apps up-to-date. Homebrew is a commandline app so I'm pretty sure its links are actual symlinks. The link shows up as "Symbolic Link (Intel:64)" in the Get Info window and looks like every symlink I've ever seen when I ls -l in the Terminal:
Are you using the Find All Applications catalog item or the Applications folder one? The former works for me, but (a) it finds the application itself in /usr/local/Cellar, not the symlink in /Applications (which is okay) and (b) it also finds hundreds of apps that I want neither to index nor to have to manually individually deactivate.
The Applications folder catalog item still does not find symlinked apps at all.
Granted: I'm in a slightly weird situation because I have an SSD and an HD that I'm in the very leisurely process of migrating from, so many apps exist in both places. This contributes to the "hundreds of apps I don't want to index" problem.