Lesson 1: DO NOT rely on seat maps to tell you availability with any level of precision. Sometimes seats look occupied when they are in fact empty, and other times seats look empty when they in fact will be occupied. You have to use the inventory class availability to get a sense of how empty/full a flight really is.

I presume you are looking at a flight from US to either Canada or Caribbean/Mexico/Northern S. America. On these flights there is technically no BusinessFirst, which books into J, D or Z. Instead, it is just plain Business Class, which books into C, D or Z. "A" class is for domestic First Class flights.

Most likely because the service you used didn't have enough "space" to display all the fare classes. If you are looking for a specific fare class, you'll probably need to use a more robust tool that allows you to specifiy a fare class, such as KVS or ExpertFlyer.