The location: Yacht Club Restaurant
Instead, the building that you see, when Dex first arrives in his car - the one with the sign reading "Bay Terrace", where Quinn is waiting - is located at the east end of a street called Whalers Walk (which is more like a road inside of a parking lot).
To reach the building from the Cabrillo Plaza fountain (where they filmed the earlier bloody crime scene), you drive past the fountain and turn right (east) into the parking lot on Whalers Walk. Drive east to the very end of Whalers Walk, and it's the big, two-story building in front of you to your left. A large sign outside says 210 - Berth 31, and lists a number of yacht dealers.
They changed that sign to read "Bay Terrace" for the scene, used some color flood lights on the walls, and added a name banner to the second floor balcony.
There are several different locations in this scene - clustered in the same area: The restaurant building, the spot where Zach parks, the marina gangway where Zach's father enters with Sofia, the building Mr. Hamilton walks past when Zach was stalking him, and the spot where Dexter captures Zach with his hypodermic. (You can see the exact locations on this aerial photo map.)
The first location is the yacht club / restaurant building: (The camera here is looking northeast)
The second is the marina gate (29-C) where Mr. Hamilton & Sophia walk up a gangway, then kiss.
(The camera here is looking southeast)
The third location is the small, low building that Mr. Hamilton walks past, while Zach is stalking him.
And the fourth is the corner where Dexter captures Zach, moments before he would have killed his father.
(In this photo, the camera here is looking south, towards the marina slips.)
Q. How the heck did you figure out where it was?
A. They filmed the earlier crime scene
(with Zach) here at the Cabrillo Marina, so it was obvious that this
night scene was also shot somewhere in that same marina complex.
The only problem was pinpointing which buildings they used, since many
of them tend to look alike.
Fortunately, this particular
building (the one used as the yacht club restaurant) has a unique
flower-shaped keyhole window on its west side, which is visible as
Dexter drives past the yacht club at the start of the scene.
So it was just a matter of using aerial photos to look at the various buildings until I found the one with the window
that matched. There is no Google StreetView on Whalers Walk, but
fortunately there is Bing's StreetSide View, and that allowed me to get a
great look at the building. And then I drove down there to verify
it, and to shoot the photos you see above.
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