Most of the cheap SATA cards you can buy have absolute garbage controllers and if you mix them with absolute garbage drives, some terrible failure scenarios occur, I've seen one failing drive take out a whole card, constantly knocking several drives offline in my RAID6 array. This was an absolute hell staring at smartctl and RAID repairs every few weeks until I finally gave up and swapped the controller, once that was done, the single drive failed cleanly and got kicked out without knocking the whole array offline.

What you are describing though sounds like a SATA card with a port expander. Most normal AHCI cards are fairly decent and the ports are independent. So loss of a single port won't take the whole thing offline. This is basically the same setup you have for the motherboard ports.