She can travel directly to Thailand on an expired passport. Countries can't refuse permission for citizens to enter.A valid passport gets you into OTHER countries.
Your baby will be stamped in for 45 days but don't worry about the overstay. Children are never fined and she won't enter Thailand again on that passport.
Nippon Air probably partners with either Thai Airways or Bangkok Air domestically. Then they could give you both boarding passes at checkin. Then your luggage would go straight through and you would use the transfer facility. Just follow the signs.