It's not that their votes just weren't counted. Southern states that declared secession chose not to participate in the U.S. presidential election of 1864. The states that had declared secession believed that they had formed a new nation, wholly separate from the United States. They had set up their own government with their own president, and, as far as they were concerned, had no reason to participate in the U.S. election. Why would they? They believed that it wasn't their government anymore. I'm not aware of any situations where a Southerner attempted to vote in the election, but since elections would have been managed by state governments, there most likely wouldn't have been any opportunity to cast a vote even if someone had wanted to.

The Southern states that declared secession had formed the Confederate States of America and elected Jefferson Davis to be their President in February 1861 under the Provisional Confederate Constitution (and again under the Permanent Confederate Constitution in February 1862). Under the Confederate Constitution, the President served a term of 6 years, and was not eligible for reelection. This meant that the next Confederate presidential election would have taken place in 1868. However, the Confederate government was dissolved following the South's loss at the end of the Civil War in May 1865, making Jefferson Davis the first and only President of the Confederate States of America. Confederate states had held midterm elections in 1863, but there were no national Confederate elections in 1864.

It's worth remembering that one of the immediate causes of the U.S. Civil War was that Abraham Lincoln was elected President even though he did not appear on the ballot in 10 Southern states. It's entirely possible that even if the Southern states had somehow chosen to participate in the election of 1864 (which would have been extremely complicated given the ongoing war) Lincoln may have won reelection anyway. The important point here is that the Southern states weren't simply ignored in 1864 - they actively chose not to be a part of the United States government.