Most rackmounts are designed for high static pressure (i.e. "forced") air cooling. This most certainly applies to the storage chassis units, where the amount of air available for cooling is relatively minimal because you have 12 or 24 drives nearly blocking the way, and the fans are working hard to overcome that, using what is perhaps a millimeter gap above and below the disks in order to bring in airflow to cool not only the drives, but also the rest of the system.
The Supermicros, when combined with appropriate mainboards and IPMI settings, are actually kind of quiet compared to some other gear once they've booted and settled down, but I would not give them points for "quiet". On the other hand, the SC846 here is quietER than the stack of three ethernet switches in the rack plus their redundant power supply, which emit a steady dull roar.
Ultimately you have to deal with the heat somehow. Not using a chassis that has the drives stacked in an airflow-resistant manner gives you more opportunity for passive and low static pressure cooling strategies. We have some nice ESXi nodes that are very quiet because they were built in a 4U chassis, with variable speed fans, a massive heatsink on the CPU, and no hot 3.5" drives (all 2.5" HDD and SSD). Low heat means the fans run slow. Oversized heatsink means that even when the CPU is running full tilt, it can throw away the heat easily and the fans don't need to rev. Most providers would stick these in 1U or as part of a blade server, but then they'd require a lot more to keep them cool.
