Well, it was always like that, i.e. not managed by the government directly, so one of the reasons is some kind of tradition, I suppose. From Wikipedia.
Sandia Laboratory was operated by the University of California until 1949, when President Harry S. Truman asked Western Electric, a subsidiary of American Telephone and Telegraph (AT&T), to assume the operation as an "opportunity to render an exceptional service in the national interest." Sandia Corporation, a wholly owned subsidiary of Western Electric, was formed on October 5, 1949, and, on November 1, 1949, took over management of the Laboratory. The United States Congress designated Sandia Laboratories as a National laboratory in 1979. In October 1993, Sandia National Laboratories (SNL) was managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin. In December 2016, it was announced that National Technology and Engineering Solutions of Sandia, under the direction of Honeywell International, would take over the management of Sandia National Laboratories beginning May 1, 2017.
As for the implications, I'll let someone else comment/answer, for now... but I'll say that Sandia doesn't seem the only one. From an article lambasting this policy:
Several years ago, the U.S. Department of Energy put management of our nuclear weapons research and development labs out for bid. Against the advice of many, DOE awarded the contract for both labs (Lawrence Livermore in the Bay Area and Los Alamos in New Mexico) to a single private partnership comprising the University of California Regents, Bechtel Corp., and other private companies. This created the Holy Grail of unaccountable profiteering: Not just a for-profit monopoly, but a taxpayer-funded for-profit monopoly.
For a more nuanced/opposing view, a 2004 paper notes:
the development of the market-based management system of the U.S. Department of Energy (DOE) multiprogram (national) laboratories-the government-owned, contractor-operated (GOCO) system-is well over 50 years old, dating from the Manhattan Project. During the Manhattan Project, the World War II effort culminating in the development of the atomic bomb, the federal government asked the University of California to operate what is now Los Alamos National Laboratory. This was the model for GOCO management of laboratories, with the government owning the laboratory site and its equipment and buildings but with the contractor-the university-providing the employees and managing them.
[...] the GOCO system is quite distinctive and, from an organizational standpoint, a design innovation. During the past 50 years, the GOCO model spread throughout DOE and its predecessor agencies (e.g., the Atomic Energy Commission) and has been used in other government agencies as well, including the Department of Defense. Currently, GOCO arrangements are used to manage 19 U.S. laboratories, nearly a dozen manufacturing and production plants (for weapons materials, components, and assembled devices), and repositories such as the Strategic Petroleum Reserve. [...]
A formal statement of the structures and criteria for a GOCO laboratory is set forth by the Office of Federal Procurement Policy (1984). The GOCO contractor may be a university, a for-profit corporation, a not-for-profit corporation, or a consortium combining such institutions. The selection of the management and operations (M&O) contractor takes place in either an open competition with all bidders welcome or in a restricted competition with prequalified bidders. [...]
The advantage of the GOCO system-at least as seen by officials of the largest GOCO lab, Sandia National Laboratories-is a streamlined bureaucracy, although the GOCO labs have nonetheless been highly criticized as too bureaucratic (U.S. DOE, 1997):
The GOCO allows proven private-sector processes to operate without bureaucratic restrictions and procedures that sometimes exist within government institutions. One particular characteristic of the GOCO concept has served the nation well: scientific independence. Scientists performing for a GOCO contractor are to a great extent insulated from political pressures. As a result, they can speak out as honest brokers, acting truly in the national interest. (Sandia National Laboratories, 2004)
In actuality, the GOCO system is not so clear-cut. It is an evolving management innovation, or set of innovations. The nature of the GOCO system has changed radically since its inception and, even today, is implemented in very different ways at the various laboratory sites. As W. Kenneth Davis notes in his brief history of the GOCO system at the Department of Energy, "It is important to note that they evolved in a way dictated by circumstance" (National Academy of Engineering, 1994, p. 224) [...]
The original GOCO arrangement for managing a federal laboratory was at the behest of President Truman. Truman's letter to AT&T president Leroy Wilson requesting that AT&T manage what later became Sandia National Laboratories made an appeal to the national interest. AT&T accepted and began managing Sandia on November 1, 1949. Other GOCO arrangements were set up at about the same time including, among others, the University of California's management of Los Alamos (the first GOCO contract), General Electric's management of Oak Ridge National Laboratory, the University of Chicago's management of Argonne National Laboratory, and Columbia University's management of the new Brookhaven National Laboratory. The original contracts were little more than a handshake agreement; early contracts were based on a dollar-per-year fee and were motivated chiefly as a public service.
From this beginning, the GOCO system spread to other national laboratories created in the 1950s (although on a management fee basis rather than as dollar-per-year public service). The presumption in the early years of the GOCO system
was that the private sector could more effectively manage research support (as demonstrated in the Manhattan Project) and leave the science to the scientists. The early contracts assumed cost recovery and mutual scientific exchange and benefit but were not viewed as profit centers for the contractor-managers. In later years, especially within the past decade, the GOCO system has been subject to contract reform and privatization initiatives that are closer to traditional market philosophy. The GOCO contracts are now subject to a required rebid on a periodic basis (as opposed to a previous system of change only for poor performance or at contractor discretion). The amount of the fees collected by contractors has skyrocketed in the past decade as their liability has increased in connection with laboratories' hazardous waste disposal problems, among other cost issues.
That 20-y.o. paper possibly doesn't cover later changes, but it gives a broader picture of how the system came about in its early years.