Regarding "Way's Packet Directory," in the several Civil War remarks Frederick Way wrote in his thumbnail histories of individual riverboats I have found some errors. After all, Way's interest was in the history of the riverboats of the Mississippi River system, and not in the Civil War. It seems he passed along a few Civil War remarks as he found them with no way to corroborate them. To me, this hardly diminishes the value of his work at all, but I have the advantage of other materials to consult.

The "St. Joseph Weekly Herald" is available on microfilm for all of 1864 and past. I cannot recall how much of 1863 it covers or any before in the microfilm rolls. It comments occasionally about river traffic. You can view it via Interlibrary Loan. Regarding the Missouri Civil War newspapers, I found that only those papers that were in river towns covered river traffic with any regularity and accuracy. For example, the Fulton and Columbia weekly papers don't have much at all except for large events. Here are others:
-- There are three daily St. Louis papers that are available, and I have used the "Republican" and the "Democrat." I have not used the German-language newspaper nor have I used the fourth paper--the "Union", I think it's called. The St. Louis "Daily Missouri Democrat" and "Daily Missouri Republican" have a lot about river traffic.
--The "Kansas City Daily Journal of Commerce" is also available on microfilm for all the war and covers the riverboats well, too.
--The Boonville weekly survives in all or part, but I have not seen it, so I cannot give details.
--The Jefferson City "Missouri State Times" survives on microfilm, but I cannot recall how it covers the boats.
--The "Lexington Weekly Union" survives and has some boat information.
--A number of issues of the "Central City and Brunswicker" at Brunswick in Chariton County survive on microfilm, but I cannot recall if it covers river business.
--Some of the Leavenworth papers survive but you would have to find those in Kansas or Kansas City. I would check first with the Kansas City Public Library for that, as they have excellent research facilities and are very helpful.
That's all I know about surviving Civil War newspaper issues along the Missouri River. Part of the reason the other newspapers stopped printing during the war was martial law, as you said, and part of the reason was that Union troops attacked the offices and presses of any newspaper uncomplimentary of their side. That happened in a number of towns.

I seriously doubt that rumor you heard that Lane's raiders destroyed a river vessel at Osceola in their 23 September 1861 raid that devastated the town. I checked some sources of that event that include a lot of detail with no such mention. About the most detailed is Kathleen White Miles' 1971 "Bitter Ground: The Civil War in Missouri's Golden Valley (Benton, Henry and St. Clair Counties)" published by The Printery of Clinton, MO. Miles devoted pages 125 through 155 to various first person memoirs of residents of the raid. On page 146 Miles quoted Dr. J. Wade Gardner:

"Osceola then had no railroad, but was the head of navigation on the Osage River. Two mercantile firms of Osceola then each owned a large steamboat, and these boats, when the Osage river was in proper condition, constantly plied between Osceola and St. Louis."

Since the doctor offered that much, I think if any such vessels were destroyed by Lane's men, it would have been noteworthy. The problem is that I believe we are trying to prove a negative here, and that is hard to do. It's like that time when I was in the Army that I presented some half-wit commander's case that a soldier should be discharged for "extreme apathy." The Army couldn't figure out a way to prove that, the man was actually an okay soldier, and with his three good attorneys he beat the case (and made mincemeat out of the half excuse for a case that the Army gave me to present). So you see, proving or disproving something that was never there is really hard to do.

I hope this helps. I enjoyed putting it together for you.

Bruce