I am interest in the missing part: what data structures/layouts are used inside LDB? Cause for In-Memory DB, CPU cache miss plays a key role in executing query. And how much data are touched to execute a single query in common case?

Cache misses are not compared to initializing the lisp engine. So, we don't worry so much about them. Also, since the data organization is up to us, we touch only what is necessary (well, almost! We are talking about fine-grained locking here, but we modify (mutate) only the datum that needs to be changed).