From the schema it looks like this is storing nodes and lines: https://github.com/osmzoso/pbf2sqlite/blob/main/doc/pbf2sqli...

There's an option to enable RTree indexes to speed up queries like this one:

  SELECT way_id
  FROM rtree_way
  WHERE max_lon>= 7.851 AND min_lon<= 7.854
   AND  max_lat>=47.995 AND min_lat<=47.996;