Later, wider suspensions of habeas corpus came later after the congressional vote.
Your post might leave the impression with some that outside of the two suspensions of habeas corpus in your link that Lincoln didn't suspend habeas corpus in other places and in wider areas until after Congress in 1863 authorized him to suspend habeas corpus. To correct that possible misinterpretation, here are some other occasions that Lincoln and others suspended habeas corpus:
April 13, 1861. US Army Colonel Harvey Brown leaves a proclamation suspending habeas corpus in Key West, Florida with Bvt. Major W. H. French commanding Fort Taylor in Key West with instructions to use it if needed and saying that "its legality has been determined by higher authority." [Source]. I wonder who that higher authority might be who issued such a order even before Colonel Brown sailed to Key West with the Fort Pickens expedition sent by Lincoln in April. I wonder who authorized a mere Colonel to authorize a mere Bvt. Major to suspend habeas corpus.
April 27, 1861. Lincoln issues his suspension of habeas corpus between Washington DC and Philadelphia. You kindly provided a link to that proclamation.
May 6, 1861. Bvt. Major French posts Colonel Brown's proclamation suspending habeas corpus in Key West. French also suppresses an newspaper in Key West, the "Key of the Gulf" newspaper, certainly one of the first of many newspaper suppressions in the North and South by the Union during the war. [Source].
May 10, 1861. Lincoln issues a proclamation suspending habeas corpus in the islands of Key West, the Tortugas, and Santa Rosa. [Source].
June 20, 1861. Lincoln authorizes General Winfield Scott or any officer he designates to suspend habeas corpus in the case of Major William Henry Chase, who resigned from the US Army in 1856 but had become a major general of Florida State Troops in the Confederate Army in 1861. [Source].
July 2, 1861. Lincoln suspends habeas corpus between Philadelphia and New York City. [I've seen a number of references to this suspension but haven't found the actual wording].
October 23, 1861. Lincoln suspends habeas corpus in matters relating to the military in Washington, DC. [Source].
December 2, 1861. Lincoln suspends habeas corpus in Missouri. You kindly provided a link to that proclamation.
August 6, 1862. Lincoln suspends habeas corpus throughout the US for cases involving discouraging enlistment in the military, aid to the enemy, and persons arrested for disloyal practices. This proclamation orders that "no citizen liable to be drafted into the military service, be allowed to go into a foreign country." The proclamation was issued for Lincoln by Stanton. [Source].
September 24, 1862. Lincoln issues a nationwide proclamation covering much of the same ground as the one issued in August, but without the prohibition on leaving the country. However, the August proclamation still remained in effect. [Source].
The above list came from my cursory search for Lincoln's suspensions prior to 1863. There may be some other suspensions in this period that I missed.
:)