The without prejudice part is in the article:
The DOJ had asked Ho to toss the case “without prejudice,” which would have allowed charges to be refiled against the mayor in the future.
As for why that could be bad:
Ho, in his order on Wednesday, wrote that dismissing the case without prejudice “would create the unavoidable perception that the Mayor’s freedom depends on his ability to carry out the immigration enforcement priorities of the administration.
The judge also said it would create the perception that Adams, who is seeking re-election this year, “might be more beholden to the demands of the federal government than to the wishes of his own constituents.”
“That appearance is inevitable, and it counsels in favor of dismissal with prejudice,” Ho wrote.
CNBC doesn't mention it, but other coverage says China has filed a complaint with the World Trade Organization. It's weird how little the WTO comes up in relation to Trump's trade war.