Question: I have my D7000 set to use its second SD Card slot to back up and I am shooting in raw (NEF). 

Every image is shown twice in playback mode, and when the images are imported to Photos (MacOS). This makes deleting individual images a pain. 

As it is copying the images to both cards it makes some sense, but the menu says "backup" not "duplicate" so I would at least expect the internal firmware to understand and not show the images twice. 

To clarify a little, when in playback/review mode, I see the images in chronological order, first for card 1 then again for card 2, so if I have taken images A, B and C I would see A1 -> B1 -> C1 -> A2 -> B2 -> B2 (1 and 2 represent the card slot).
So to delete image B I have to delete two images, once for each card.

Is this normal behaviour?

Firmware is
A 1.04
B 1.05
L 1.002

Answer: 
After the clarifications, what you describe is normal behavior. I simply leave the backup card alone and format it entirely when I am certain I won't need the backup copies. If you are concerned that the card(s) will fill w/ unwanted pictures and stop being able to record then I would just get a larger backup card (2-4x the size of the primary card).
Have you [chosen a memory card slot for playback](http://download.nikonimglib.com/archive2/j0v3l00Dv39x01U97ft13W9kOV17/D7000_EU(En)06.pdf) (page 164)? Otherwise (page 163) "The most recent photograph will be displayed in the monitor", which I'm taking to mean in chronological order irrespective of card slot.

"Photo apps" is a very broad term, but if your software is importing everything from the camera it may also be adopting a chronological display order.

You might be able to get round this by manually selecting only one card slot for import, or by copying files from one card only to the directory used by the software.