No doubt that's true -- Maryland, Western Virginia, Kentucky and Missouri, to name a few, all supplied substantial troops to the Confederate Army.
How many they supplied, and what percentages went South versus North is probably debatable.
Somewhere I saw numbers for Maryland suggesting two served the Union for every one in the Confederate Army -- or more-or-less the reverse of Confederate states like Tennessee and North Carolina.
As for more sympathetic "Doughface" Northern states, like Pennsylvania, Indiana and Illinois -- I've never seen numbers, if there are any, on Confederate troops from those areas.
Enlistment records in the South were not bad as I understand it, it is just that all the data was stored in Richmond with no duplicates anywhere and it all went up in flames.