I think even when I was quite young, in the late 70s/early 80s, I assumed that the rules also applied to NPCs. Partly because of the reference to military units, which didn't seem straightforwardly applicable to PCs.Note that the rule doesn't reference NPCs...
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Classic Traveller is the only game I'm aware of where only players are mentioned in the morale rules...
(noting that animals have a different morale equivalent.)
Not that any Traveller ref I've known has limited it to PCs...