Launching nautilus from command line and launching nautilus via D-Bus (from web browser) are 2 different things.
- The former is a simple direct command launch. Refer nautilus-application.c for more details.
- The later involves mime type processing and selecting 1 app from apps supporting the freedesktop.org File Manager DBus Interface. Refer nautilus-freedesktop-dbus.c for more details.
It appears that nautilus does not open a new window for the same URI when launched via [2], though this always works with [1]. This might be a conscious decision to not launch too many windows which might clutter the desktop. In most cases, it makes perfect sense.
If you’d like to always open a new window, I’d look into discussions in this recent thread. I would create a wrapper shell script around nautilus if necessary.