A few people were playing cards. So in the end the person who lost thought that "a few cards were missing". So can be expressed as:
This was not a full deck.
The deck was not full.
What sounds natural #1 or #2?
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Both expressions are correct and mean roughly the same thing. The pronoun would more likely be "That wasn't a full deck". Or "That deck wasn't full". Since the deck has been used and so is psychologically distant from the speaker.
You would be more likely to express this as opinion "I don't reckon that was a full deck." or "There's no way that deck was full, I was waiting for the 8 of clubs the whole game".
You can say "One card is missing", but you can't say "One card is less" The word "less" doesn't describe the card.