Morale still resets on game reload, at least when you reload an in-port save. I also noticed that reloading in-port saves causes the characters in the bunker to "lose" their names - the flottilla commander and technical officer are introduced as "JOB RANK name".
However talking to crew will now at least build their morale back up from that.
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There are only forty people in the world and five of them are hamburgers.
-Don Van Vliet (aka Captain Beefheart)
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