So, this came trying to fix a little issue.
Christian Hegert pointed to me that nautilus -s was not working
all the times. It was working only when the application was already
running.

That's because there was a race condition in the dbus.
We were starting nautilus, owning the FileManager1 dbus path
and inside application_select we were calling the dbus method
to select the items. Then that instance died and the dbus path
became unown by Nautilus again, but we were in the middle of a call
to the dbus method. So that created a race somewhere and Nautilus
was not responding to that call.
When there was an instance already alive this was working fine since the
dbus path was owned by Nautilus already.

So one solution was to instead of calling nautilus by a dbus call for
that use case, directly do the need operations there. But then it was
happening the opposite, it was working for the first instance, since the
startup is called an everything is in place, but when created a second
instance with the -s option it was crashing because the second instance
was not initialized and nothing was set up for it.

So finally, the solution I though is better for this is always handle
the command line options on the main instance.
A way to do this is connecting to the command-line signal of
GApplication and drop handle_local_options and application_open.

Doing this actually make things easier for everything, like the problem
we had some months ago about nautilus creating one window when icons on
desktop was activated. That was happening because depending on the
return value on handle_local_options it called the activate signal or
not.
Now instead we manage everything as we want in the handler of the
command-line signal, so we don't have to worry about those things
anymore and the code becomes clearer and simpler.