What is the value of option
dired-listing-switches? If you are telling
ls not to list dot files ("hidden" files) then they will not be shown by Dired.
Do you have
dired-omit-mode turned on? If so, what are the values of options
Even with vanilla Dired, file names with extensions such as
.git are matched by the default value of
dired-omit-extensions, so they will not show when
dired-omit-mode is turned on.
Do you see the same behavior if you start Emacs without your init file:
emacs -Q and you use only vanilla Dired? If you start Emacs without your init file and you use Dired+?
Dired is quite configurable, and Dired+ is even more so. Whether to show such files is up to you.