Does the OS recognize all 5-6 cores in the Apalis iMX8?

The Apalis IMX8 lines have a cpu with 2 different microarchitectures.

1-2x Arm Cortex™-A72 @ 1.6GHz
4x Arm Cortex™-A53 @ 1.26GHz

Does the OS recognize the 6 Cores or do I need to program it differently like you would with the MicroController?

If the OS recognizes all 6 cores, does the CPU automatically adjust threads to faster cores like Intel Boost?

Yes it does recognize them and assigns tasks to cores automatically. You can check it by using htop command.