I didn't find Lost overly religious at all. There were some basic principles that are found in many world religions, good/evil (or just bad), forgiveness, sin, etc. I actually though there would be a bit more to the Jacob story, but I never thought that he and his brother were gods or God and the devil or biblical persons at all actually.

I felt that the religious items in the room were a nod to the various beliefs and possible beliefs of the viewership and characters.

With regards to the bomb... The obvious thing it did was unify the timelines. As to "why" it did that... Anyone's guess I suppose.

Originally the island's current inhabitants were popping around through time and that stopped when Locke moved the wheel. WHy did the island start jumping around in the first place instead of only moving once? Don't know. Why did spinning the wheel again stop it? Don't know, but that's easier to fathom if you think about the wheel as a switch of some sort.

So setting off the bomb reset the timeline. Somehow.

I'm drawing a bit of a blank here... Did we ever see Frank Lapidus in the limbo scenes? That's what I'm going to call it from now on I think - some people have been calling it purgatory, but that's specifically a Catholic concept and doesn't describe what the characters were doing in that part of the series.

Smoke monster - the soul of the man in black, trapped on the island, ripped from his body when he went to the light. Question: Why didn't Jack die the same way?