Spotlight isn't putting that file there; that's where the Finder stores the directory-specific preferences (window size/position, list vs icon display etc). If you don't use the Finder (which I mostly don't) then you'll never see these files.
I have this at the bottom of my .zshrc just for this reason:
# remove any .DS_Store files
# (run in a subshell to suppress background job number info being printed)
( ag --hidden -u -l -g '\.DS_Store$' |xargs -n 1 rm -f & ) > /dev/null 2>&1
Spotlight maintains its own database in /