I'm not sure what command the Cmd+Shft+. shortcut invokes, but to truly show hidden files (on 10.9.* through 10.13.*, as of today), use terminal to execute:
defaults write com.apple.finder AppleShowAllFiles TRUE; killall Finder
For 10.6.* through 10.8.*, use (note the capitalization difference in the first instance of
defaults write com.apple.Finder AppleShowAllFiles TRUE; killall Finder
(I'm definitely not a fan of osxdaily.com, but it works.
Additionally, to check on your current value, use
defaults read com.apple.finder AppleShowAllFiles
... and for simple usage of the
defaults command, just enter
defaults with no arguments.
I verified that the value on this system is set to
TRUE and I can see all the .DS_Store files as seen below... (using 10.11.6)