Many questions asked so this one is a bit longer, bear with me. :)
Day 2 (12/24) Train to Ljubljana (8:00 - 14:00) Will everything be closed by the afternoon? Recommended churches for Christmas Eve?
Shops and other businesses might close early, but not before 16:00 or 17:00 I don't think. Museums and sights will mostly remain open. For Midnight Mass you should probably head to the Cathedral of St Nicholas or to the Franciscan Church on Preseren Square. The Christmas Market in Ljubljana is open until January 5, so it will be open until late on Christmas Eve, Day and Independence Day. There are outdoor music performances, choirs singing etc. in the squares and streets. For street theatre performances, follow the riverfront south from the Old Town to Spica point at the confluence of the Ljubljanica River and the Gruber Canal, where the Ana Mraz festival takes place from December 26 to December 30.
Day 3 (12/25) Quite day in Air B&B near castle. Restaurants open?
Many will be open and I wouldn't be surprised if reservations were essential, although I can't say for sure. I don't eat out in central Ljubljana on Christmas Day, I usually go to the countryside and we always book ahead if we decide to go out for lunch there. Note that eating out on Christmas Eve is not that common.
Day 4 (12/26) Independence day - Will restaurants and other businesses be closed?
It's a public holiday, many shops will be closed but the Christmas Market will be open, as will many restaurants.
Day 5 (12/27) Day trip - how far north can we go this time of year? We would like to see Soca valley, alps?
Day 6 (12/28) Day trip Bled, Bonhinj?
Day 7 (12/29) Karst area (Skocjan and/or Postojna caves, Predjama Castle)
You can go as far north as you'd like, the mountain passes will stay open unless there is avalanche danger. However, I don't think you would want to go too far; the end of December isn't the best time for a day trip to the Soca Valley. The sun will rise at 8:00 and set just after 16:00 and in the mountains daytime is even shorter, leaving you with little time to explore, not to mention the possibility of inclement weather. Natural sights won't be as appealing during that time either, with many hikes becoming dangerous due to ice or snow. Note that trails are not controlled so it's not common for them to physically close except for places like the Vintgar Gorge, it's up to you to be aware of the conditions and not set off unprepared.
Lakes Bled and Bohinj will be gorgeous if covered in snow and from Lake Bohinj you can take a cable car up to Mt Vogel for wonderful views of Mt Triglav in clear weather. You could also partake in some winter activities, as it is a ski resort in the winter. I'd also include a stop in Radovljica, a lovely medieval town just outside Bled. Many winter activity options elsewhere in the country, too.
Postojna Caves feature a living nativity scene performance through December 30, I'd go see that. Check online for times and tickets ahead, it's quite popular. Another day trip idea is Trieste on the Italian side. This area is also the best area to do hiking in the winter, as snow is much less likely in the southwest, except for Postojna, which usually gets more snow than Ljubljana. I personally enjoy the Rilke Trail along the coastal cliffs near Duino, north of Trieste, it makes for a lovely afternoon walk in the winter sun or a stroll through Piran can be enjoyable if the sun is out.
Generally, with regards to day trips I'd play it by ear. See if there are any events that spark your fancy and follow the local weather forecast. A rental car would be a good idea to move around to maximize your time in the daylight hours for sightseeing etc. Rentals are equipped with snow tyres in winter.