The officials do not think their sources have been compromised or killed – rather, they've been spooked into silence amid "more aggressive counterintelligence by Moscow, including efforts to kill spies," according to the Times, pointing to the still-unsolved March poisoning of former Russian double-agent Sergei Skripal in the UK.
Curiously, the Times immediately suggests that the lack of intelligence is "leaving the CIA and other spy agencies in the dark about precisely what Mr. Putin's intentions are for November's midterm elections."
But American intelligence agencies have not been able to say precisely what are Mr. Putin's intentions: He could be trying to tilt the midterm elections, simply sow chaos or generally undermine trust in the democratic process. –NYT
There it is. Of course, buried towards the end of the article is this admission:
But officials said there has been no concrete intelligence pointing to Mr. Putin ordering his own intelligence units to wade into the election to push for a certain outcome, beyond a broad chaos campaign to undermine faith in American democracy.
Meanwhile, "current and former officials" tell the Times that the outing of FBI spy Stefan Halper, who infiltrated the Trump campaign, had a "chilling effect on intelligence collection."