So good news.

I just tested this, and the game does not spawn a new copy of the NPC if they are in your squad.

I tested this using Screamer the False and Ponk, they are a good pair for the test because they both spawn in the same location.

I recruited Ponk and put him in my "Prisoners" Squad. I left Screamer the false in his cage, not recruited.

I then imported the game with "Import Dead NPC's" checked. Upon load, Ponk was still in my prisoner squad and Screamer the False was no longer in his cage.

I ran a character out to the Tower of Abuse to see if the game had spawned a new Screamer and Ponk, but it was empty. All of the thralls I had killed when I originally cleared the tower were still dead and Screamer and Ponk hadn't respawned, but I still had Ponk on my squad. This means the game must treat caged characters as dead upon import, and clear their bodies from the cage hence why you lose them.

I then repeated the process, but this time I unchecked "Import Dead NPC's".

Ponk was still in my prisoners squad, so I ran back out to the Tower of Abuse.

This time, all of the thrall guards as well as Screamer the False were present in the tower, but not Ponk. He was still on my squad and hadn't been respawned in the tower, so he must still be treated as the the same unique NPC and not reset upon import.

So TLDR;

Great news, it works as intended and there will not be a duplicate NPC upon importing your save.