Greetings, and welcome to the Boston area
1. I ride in Boston after dark almost every day (and I pass within a mile of the BI), and generally feel much safer on a quiet night than in daylight (and rush-hour) hours. As long as you have good lights, know the area, and avoid heavily-trafficked intersections (as much as possible), you'll have no problems.
2. I commute year-round. I do live right on the T, so if the weather really sucks I'll take the train in. In the past year, I've done that about three times.
3. It's done as often as someone finds it useful
You can take a bike on any of the subways except the Green Line, or during rush hour. I've seen bikes on the T before, it's not terribly unusual.