Earlier quoted context omitted.
Protobuf is not a database. What comes close is DataDraw, but that is an embedded database, not a server.
I don't understand your meaning, then... lots of database systems have hardcoded fixed pointer offsets for data structures, and some even compile queries into bytecode with those hardcoded pointer paths (for instance, HyPeR does this using LLVM, and I think some other column-stores do as well). Is your issue that those databases aren't hierarchical? On modern machines, pointer chasing is much slower than predictable…
DataDraw is kinda similar, but in memory. There is a reason why it doesn't have a generic SQL interface, although it would be probably possible to build a slow one on top of it.
P.S. I don't know HyPeR, and I can't google it. And yes, it's possible that somebody already reinvented IMS, I am just not aware of it.