I couldn’t find a list, just mention of some of the larger and more well known papers.
“You will take possession by military force, of the printing establishments of the New York World and Journal of Commerce . . . and prohibit any further publication thereof . . . You are therefore commanded forthwith to arrest and imprison . . . The editors, proprietors and publishers of the aforementioned newspapers. (Order of Abraham Lincoln to General John Dix, May 18, 1864)”
That still leaves us 298 newspapers short.
And the reason why the Journal of Commerce and the World were ordered shut down was because it was believed, erroneously as it turned out, that they were complicit in a financial fraud and not for political reasons.