I'll be honest here. I don't care about the yao guai or mirelurks. I'm sure they have their own special reasons as to why they became what they did. Obviously we know what yao guai are and how the got changed so that's a no-brainer. Mirelurks are weird but they remind me of those weird ancient fish things, you know the ones with all those feeler legs or some such. They're a shell-fish of sorts anyways. As for Rivet City-it was probably sitting in the harbor when the bombs hit which would explain why the aircraft are still present there. It also means that people in DC had no idea what was coming, otherwise all those jets would have been dispatched to attempt to misdirect the bomb or bombs.
EDIT: Perhaps the mirelurks come from something like this: http://www.flickr.com/photos/fossilmike/2660602184/in/pool-trilobites
there is a terminal in fallout 3 that says mirelurks came from horse shoe crabs and this one other crab (dont remember the name i think it was like blue crab or something)
its in an enclave outpost
oh and the mirelurk kings remind me of the deep ones from H.P lovecrafts stories
ill quote a description of them
"I think their predominant color was a greyish-green, though they had white bellies. They were mostly shiny and slippery, but the ridges of their backs were scaly. Their forms vaguely suggested the anthropoid, while their heads were the heads of fish, with prodigious bulging eyes that never closed. At the sides of their necks were palpitating gills, and their long paws were webbed. They hopped irregularly, sometimes on two legs and sometimes on four. I was somehow glad that they had no more than four limbs. Their croaking, baying voices, clearly used for articulate speech, held all the dark shades of expression which their staring faces lacked ... They were the blasphemous fish-frogs of the nameless design - living and horrible."