"It" refers to the houses, the aputiak. They're entirely made of ice, so in the spring when it begins to warm, the entire house melts into water and simply disappears.
The character is saying that when a more typical house, one not made of ice, is dismantled or moved, there will always be some evidence that it was there. But the aputiak is different, because it can totally disappear.
"Landfill" in this case refers to soil that is dug out or moved for the laying of a "foundation" which is a stone or concrete platform that a house is built on top of. I'm not certain what is meant by "skips". This story seems to be written in British English because 'cozy' is spelled 'cosy' in the British style. I'm an American, so it's possible 'skips' is lingo only used in British English. But it's safe to say that a skip is something normally found near a house or dwelling.