What does the .d stand for in directory names?
The .d suffix here means directory. Of course, this would be unnecessary as Unix doesn't require a suffix to denote a file type but in that specific case, something was necessary to disambiguate the commands (/etc/init, /etc/rc0, /etc/rc1 and so on) and the directories they use (/etc/init.d, /etc/rc0.d, /etc/rc1.d, ...)
This convention was introduced at least with Unix System V but possibly earlier. The init command used to be located in /etc but is generally now in /sbin on modern System V OSes.
Note that this convention has been adopted by many applications moving from a single file configuration file to multiple configuration files located in a single directory, eg: /etc/sudoers.d
Here again, the goal is to avoid name clashing, not between the executable and the configuration file but between the former monolithic configuration file and the directory containing them.
Excerpt from a Debian mailing list (emphasis added):
When distribution packaging became more and more common, it became clear that we needed better ways of forming such configuration files out of multiple fragments, often provided by multiple independent packages. Each package that needs to configure some shared service should be able to manage only its configuration without having to edit a shared configuration file used by other packages.
The most common convention adopted was to permit including a directory full of configuration files, where anything dropped into that directory would become active and part of that configuration. As that convention became more widespread, that directory was usually named after the configuration file that it was replacing or augmenting. But since one cannot have a directory and a file with the same name, some method was required to distinguish, so .d was appended to the end of the configuration file name. Hence, a configuration file /etc/Muttrc was augmented by fragments in /etc/Muttrc.d, /etc/bash_completion was augmented with /etc/bash_completion.d/*, and so forth. Sometimes slight variations on that convention are used, such as /etc/xinetd.d to supplement /etc/xinetd.conf, or /etc/apache2/conf.d to supplement /etc/apache2/apache2.conf. But it's the same basic idea.
Generally when you see that *.d convention, it means "this is a directory holding a bunch of configuration fragments which will be merged together into configuration for some service."
For part 2, the reason for the ".d", my best guess would be "distributed", as in not part of the main configuration file, but still part of the configuration.
If you speak about ".d" at the end of directory names, this answer is right, it's just a marker for "directory".
Just don't confuse it with "d" at the and of a file name, like "syslogd", which stands for daemon. A computer process running in the background.
the parent process of a daemon is often (but not always) the init process (PID=1). Processes usually become daemons by forking a child process and then having their parent process immediately exit, thus causing init to adopt the child process. This is a somewhat simplified view of the process as other operations are generally performed, such as dissociating the daemon process from any controlling tty. Convenience routines such as daemon(3) exist in some UNIX systems for that purpose.