Here is part of the wording of the 1863 act:
"AN ACT relating to habeas corpus, and regulating judicial proceedings in certain cases. Be it enacted by the Senate and House of Representatives of the United States of America in Congress assembled, That, during the present rebellion, the President of the United States, whenever, in his judgment, the public safety may require it, is authorized to suspend the privilege of the writ of habeas corpus in any case throughout the United States, or any part thereof."
NC posted the entire bill here. It contains several clauses, one of which authorizes the president to suspend the writ, two provide indemnity against prosecution for prior acts. I don't know whether or not that implies the congress knew they could not retroactively authorize his actions or not. Maybe it's just thier way of insuring all bases are covered to preempt judicial review.