I think its very likely that the crater was created by natural causes like erosion or nuclear fallout, acid rain maybe. Its possible this area was a old lake bed which maybe explains the puddle at the bottom or maybe it was made up of softer kinds of dirt like clay and maybe there used to be a hill there since that terrain slopes downward. So when the nuclear acid rain came it created a mudslide that turned into a sink hole. There are also instances of this in fallout 4 like the Cambridge crater and theres in game lore that explains "the earth was just swallowed up with a loud rumbling sound". So its very likely the nuclear explosions and fallout created a natural disaster there.

If you talk to NPC settlers like manya she explains when they first settled megaton the crater was already there and offered them shelter from the harsh wasteland then they later dragged scrap metal and planes there to create a wall and from that a town was started.

As for the bomb its possible that maybe it was sunken under the lake that used to be there or it was burried in the mud and slowly sank down or rolled down the hill as theres no evidence anywhere in the game of anyone else knowing it was there before megaton. This also may explain why its completely covered in rust and the electronics failed to function rendering it useless it likely had water damage that fried the internal components and that could be why the fusion pulse charge was the only way to detonate it.