Hidden .DS_Store files not appearing in Finder despite enabling display of hidden files
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 Finder):

defaults write com.apple.Finder AppleShowAllFiles TRUE; killall Finder


Source: http://osxdaily.com/2009/02/25/show-hidden-files-in-os-x/
(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)