When the F.B.I. director, James B. Comey, said on Tuesday that his investigators had no “direct evidence” that Hillary Clinton’s email account had been “successfully hacked,” both private experts and federal investigators immediately understood his meaning: It very likely had been breached, but the intruders were far too skilled to leave evidence of their work.

Mr. Comey described, in fairly blistering terms, a set of email practices that left Mrs. Clinton’s systems wide open to Russian and Chinese hackers, and an array of others. She had no full-time cybersecurity professional monitoring her system. She took her BlackBerry everywhere she went, “sending and receiving work-related emails in the territory of sophisticated adversaries.” Her use of “a personal email domain was both known by a large number of people and readily apparent.”

In the end, the risks created by Mrs. Clinton’s insistence on keeping her communications on a private server may prove to be a larger issue than the relatively small amount of classified data investigators said they found on her system. But the central mystery — who got into the system, if anyone — may never be resolved.

“Reading between the lines and following Comey’s logic, it does sound as if the F.B.I. believes a compromise of Clinton’s email is more likely than not,” said Adam Segal, the author of “Hacked World Order,” who studies cyberissues at the Council on Foreign Relations. “Sophisticated attackers would have known of the existence of the account, would have targeted it and would not have been seen.”