The full-tower SM cases with the “loud” fans (FAN-0074L4) are still pretty quiet unless you are using passive CPU cooling. With the SQ fans (FAN-0104L4), it’s basically like having Noctua fans. Plus, any 80mm 4-pin PWM fan can be installed in the hot swap carrier, so there’s no need to get exotic with replacing the whole wall.
Despite the fact that Supermicro sells a version of the case with SQ fans, I wouldn’t recommend it unless you are using SSDs in the hot swap bays. With minimal airflow, spinning drives can get to 60°C pretty quick. I know…I’ve done it when testing and leaving the fans running too slow for too long.
No matter what, you’d need a fan speed control that based the fan wall speed on the drive temperature, which means something custom, as no motherboard uses external temperatures for fan control…only CPU and PCH (or other motherboard temperature sensors) are used.