Have you tried this design:

type
  Node = distinct int32

template kind*(n: Node): JsonKind = JsonKind(n and KindMask)
template operand*(n: Node): int32 = n shr KindShift

type
  JsonTree = object
    kids: seq[Node]
    atoms: BiTable[string] # store numbers as strings too and parse them to numbers in the accessor procs

The crucial idea here is that atoms use 'operand' bits to index into the 'atoms' BiTable while compound nodes use it to store the total number of children. Via some clever arithmetic operations you can easily compute the ith-child anyway. See my PackedAST code in compiler/ic.

This should be close to the optimum design. The API on top should encourage efficient operations (don't use random access, iterate over the tree instead).