Autumn trees were expected to bear fruit and so, like waterless clouds, these trees do not deliver what was expected from them. With trees being uprooted, they have been swept along by winds and there is nothing to find on them. Jude is essentially emphasizing that these heretics are corrupt and useless.
12 These are hidden reefs at your love feasts, as they feast with you without fear, shepherds feeding themselves; waterless clouds, swept along by winds; fruitless trees in late autumn, twice dead, uprooted;