This came up in a game tonight and I can honestly say its never been an issue since I've been dealing with Bossk.
The YV-666 has been destroyed, the pup deployed and is the last ship on the board. Does the opposing player get the six points for the Nashtah Upgrade or not? The opinions were split on yes vs no, 2-1.
I went through the past threads looking for an answer but came up empty handed. What makes me think that the opponent gets the points is the fact that the Pup is a "zero point" ship and the upgrade is bundled into the cost of the YV-666.
I need a more experienced opinion.