If Ohmu shell is the hardest thing around, even chipping ceramic swords, how do they cut it down to make tools etc? I know that the combination of gunpowder and relentless hacking will cut through, but that seems needlessly hard on the sword, and it seems that that would take too long to be practical.
It's clearly shown in the manga that ohmu shell is not the hardest thing around, nor is it a very durable metal. it's useful because it is easy to turn into a variety of objects and it is a purely renewable resource, unlike steel or iron.
And even if it were the hardest thing around, look at it this way: diamond is also one of the strongest materials we know, but specialized tools can still cut it and shape it. It's assumed that, once Nausicaa informed the Valley's craftsmen about the shell, that they'd go out and use the correct tools for the job and that they'd work on the actual shell, as opposed to Nausicaa's crude hacking at a weak spot (the edge of the eye dome.)
Ever notice how the door to the door leading to secret passage to the room where Nausicaa grows the not-so-deadly plants only has hinges on the inside? So, how is it able to swing inward, then outward? Much less, how is Nausicaa supposed to enter it?
The whole castle is filled with all kinds of tunnels and exits. Presumably there's at least one other way out.
How can an atmosphere with enough oxygen to support gigantic house-sized arthropods be breathable by humans? Not to mention the fact that the Ohmu, at least, are shown to have blue (hemocyanic) blood, which has only a quarter the efficiency of our hemoglobin-containing red blood. Forget the spores, everyone on that planet is going to die of oxygen toxicity.
The humans were genetically reengineered when the forest was created. Remember, the New Humans can't breathe the same air as Old Humans; that's why they can't enter the purified areas. Assuming that in this case blue blood = hemocyanin and not just nanotech that's more efficient than hemoglobin.
In the beginning of the movie, when Yupa returns to the valley, several windmills are shown - and some of them have sails rotating in the opposite direction than the ones on other mills. Is this even possible?
Yes; since the wind is pretty much constant and in the same direction, some windmills could be designed to operate clockwise and others counter clockwise.