This infographic should be a good representative of how many launches can be considered classified, so I'm reposting it here from the Collection of space exploration related infographics thread on our Space Exploration meta:
T. McCall, M. Orcutt: Space over Time / History of Space Launches
Infographic date: August 23, 2011
Of the 7,000 spacecraft that have been launched into orbit or beyond,
more than half were defense satellites used for such purposes as
communication, navigation, and imaging. (The Soviet Union sent up a
huge number, partly because its satellites tended to be much
shorter-lived than those from the United States.) In the 1970s,
private companies began increasingly adding to the mix, launching
satellites for telecommunications and broadcasting.
This graphic groups payloads by the nationality of the owner. A
satellite, a capsule of cosmonauts, or a deep-space probe would each
count as one payload. The data, which run through July 2011, were
drawn from hundreds of sources, including space agency documents,
academic journals, and interviews. They were compiled by Jonathan
McDowell, an astrophysicist at the Harvard-Smithsonian Center for
Astrophysics and author of Jonathan’s Space Report, a newsletter that
Infographic collates data on space launches from 1959 through mid 2011 and was compiled by Jonathan McDowell, a Harvard-Smithsonian Center astrophysicist, and it was designed by Mike Orcutt, a MIT Research Engineer and Tommy McCall, founder of Infographics.com, a data visualisation agency.
Why I think it's a good representative of how many space launches are classified? Because there's always going to be a debate over what constitutes a classified launch, so splitting these between military and nonmilitary government launches while including non-government launches in the numbers should provide a close enough overview, however we want to look at it. Some payloads might be only partially classified, but the point is, that with military launches, we simply don't know to what extent that is, while we can be fairly certain that with other government launches too many civilians are involved in projects to even be worth keeping any parts of them under wraps.
Please, feel welcome to adding your own favorite space exploration related infographics to our meta post where we're collecting them for easy reference. Thanks!