A couple of quick questions. My current build plan will only leave about 5mm between the top of the CPU fan and the Harddrive cage. Are there any issues with such a small gap? The second question is the plan for the hard drive cage is (currently) to use 3mm acrylic. Is that strong enough bearing in mind there will be 5 drives? I'll post some sketchup images later to give a better idea of how tight things are going to be.
As long as the fan ism't obstructed I can't see why there would be any problems . How are you planning on putting the cage together. 3mm is what i normally use for windows. For something like that I think it would be way to thin. I'm thinking of a normal type of cage in my head and thinking 5 or 6 would be a lot better.
Gap: It has the potential to be (very) noisy, but it will work. 3mm acrylic: It depends on how you build it. Two simple flat strips will likely wobble with that much weight. A slight bend or a strip fused perpendicular will strengthen it considerably.
Going with 5 is a good idea, as said it will be much more rigid. The other plus is that it will be a lot easier when it comes to glueing or screwing it all together.