You’ll find that the Emancipation Proclamation, which took effect on January 1, 1863, had the effect of freeing all slaves who came into Union lines in the Confederacy.
“Effect” are “free” are two different things. If a simple EO was all that was needed the 13th amendment wouldn’t have been.
No, they were not free, no more than any other illegal executive order is not enforceable.