Yeah, LWH, sorry.
And yes, it does make for a difference in cabin heights. Since most ships seem to have 5m decks, the heights are sort of based around a couple ideas; The Compact cabins are small enough to be stacked on top of one another, or fit in spaces where there's less height available (such as toward the hull edge on a rounded hull) the 3m height on most cabins allows a comfortable standing height for most species, but leaves room for things above and/or below the cabins such as ducts, conduits, cables, and machinery. The 5m height on the Extra Large cabin maximizes space, whether being used for storage, or for a common room, or even as a more luxurious/upscale crew cabin like a VIP room or captain's cabin.
EDIT:
And of course these are just initial suggestions. if you have better ideas and/or reasoning, I'm all for it!