Hey there, good question for sure. Here's my writeup on short ribs from my book, Modernist Cooking Made Easy: Sous Vide
Short ribs are a classic "must make" sous vide dish. Due to the high fat content they can be cooked anywhere from 131ºF to 185ºF (55ºC to 85ºC) for 12 hours to 3 days and the final dish will greatly depend on the time and temperature you use. The end result will range from a traditional braise-like texture to a chewy steak, or anything in between.
For a melty, steak-like texture, cook the ribs at around 131ºF (55ºC) for 48 to 72 hours, they are worth the wait. A more traditional, fall-apart texture will occur when cooked at 175ºF (79.4ºC) for 12 to 24 hours. A good in between texture is achieved at 150ºF (65.6ºC) for 18 to 36 hours. The longer the short ribs cook, the more tender they become so an 18 hour cook will be firmer than a 36 hour cook at the same temperature.
For #1) The bone in or out won't matter with the longer cooking times, so you are fine. When you package, make sure they are basically in a single layer and they will be fine. The thicker something is the longer it takes to heat through, so you don't want a big sack of ribs; it's better to have several sacks in one layer each that the water can circulate between.
For the second question, that's correct, just throw it in the ice bath when it is done. There are multiple ways to reheat it, from just using the sous vide bath again (for probably an hour), to heating it in a sauce or frying it. It all depends on your preparation. Just make sure you don't bring it to a higher temperature than you cooked it at originally.
Hope that all helps some. Thanks and happy cooking!