Cue Unsolved Mysteries theme song.
I assume that the SS got cryoed/suspended animationed right after the blast (I hope not, I liked the whole Life in the Vault section of Fallout 3), thereby removing the need for them to have a Pip-Boy until they got out.
If he/she has been cryogenically frozen for 200 years, what use would a Pip-Boy be? It was probably on one of the scientists who started up the cryo machines who died many years ago.
The original plan might have been for the vault dwellers to be issued Pipboys after they came out of the freezer. Whatever happened in the vault to make our character the sole survivor probably interfered with that plan. >.>
I don't think all Vault dwellers carry Pip-Boys. It seems like some Overseers distributed them to some essential personnel. Most of the Vaults and residents you encounter in the previous games do not have Pip-Boys.
If the survivors of the blast were to be put into stasis pods or frozen, they wouldn't have Pip-Boys because they wouldn't be assigned a job which would require one. The skeleton likely belongs to an administrator or technician that didn't take part in the stasis process.