Could be a little pride thing. When my W and I were separated, we each made it a point to say goodnight to the kids, EVERY night. It was an unspoken thing, but when she was going to put them to bed, sometimes she would call me to let me know and I would do the same.
By your W saying that it's not necessary to say goodnight to the kids every night, especially when they're so young, I think is rude. They need to hear and understand that their parents are still around and not just abandoning them. It's no wonder your W has a hard time with them. to them she's already checked out. They need re-assurance.
M-43 W-40 2D - 9 and 5
Emotion, yet peace. Ignorance, yet knowledge. Passion, yet serenity. Chaos, yet harmony. Death, yet a new life.