But there are other concerns to be raised on using a denormalized schema.

KiokuDB doesn't so much use a denormalized schema as it uses no schema at all. Using the DBI backend for Kioku your schema basically looks like this:

sqlite> .tables
entries    gin_index
sqlite> .schema entries
CREATE TABLE entries (
  id varchar NOT NULL,
  data blob NOT NULL,
  class varchar,
  root boolean NOT NULL,
  tied char(1),
  PRIMARY KEY (id)
);
sqlite> .schema gin_index
CREATE TABLE gin_index (
  id varchar NOT NULL,
  value varchar NOT NULL
);
CREATE INDEX gin_index_ids_gin_index ON gin_index (id);
CREATE INDEX gin_index_values_gin_index ON gin_index (value);
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