Personally I run a server and a NAS in Fractal Design cases, pretty standard (midi) tower layouts. Bigger cases need more space, true, but they also offer more space for disks, cabling and cooling. Also, the more spacious layout keeps noise down due to overall lower temps.
So if you have the room and the budget, I'd go for the bigger case.
OP, avoid N4 especially if you live in hot/humid country.
I threw mine after my HDDs overheated many times when parity check ran or prolonged r/w happened (it was > 60c if i remember correctly).
Not really feasible to remember to turn on aircon, remove the front cover, and put a fan in front of the HDDs whenever heavy read/write happens .
I have the N3. Works great, no issues cooling.
It looks like the problem with the N4 would be the clearance between the CPU and the case. You'd have to have a very low profile flat cooler, or a blower fan (noisy).
I'd check the specs and verify the actual dimensions of what you can use, and whether that would be sufficient for your use case. Remember that you also need room between the fan and case for air to actually move through.
Actually I just looked again and the top of the case is perforated, so maybe that won't be an issue? It will restrict airflow of course, but it shouldn't be that much of a problem.