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Two good cases for this are the fractal node series. Not ATX, but great.
Node 304 can do 6 HDDs, ITX board, SFX-L supply.
Node 804 is twice as big (still smaller than tower cases) but can do mATX board, 8HDDs, and an ATX power supply.
Watch out for ITX builds because they only have 4 SATA ports, so you need to get an M.2 expansion card or PCIe expander if you aren't using a video card.
mATX can usually expand via the extra PCIe connector.
I'm leaning towards the Node 804 now, and just getting an mATX board instead of an ATX one. The Node 804 can also fit a larger (160mm) CPU cooler, so my preferred cooler (Noctua NH-D15) should be able to fit if I replace the 140mm fans with 120mm ones - with the smaller fans, it needs exactly 160mm clearance.
I love Fractal Design and they seem to be one of the only manufacturers still producing older cases that can fit a lot of HDDs.