Welcome to the forums. Now, as to your questions...
1701716:can alliance deck fight against another alliance deck and horde deck against other horde deck?
Absolutely. The restrictions are simply for building the deck, not playing against other people. Think of it as a duel. You are allowed to duel your own faction.
which one of these is the best one: rogue, warlock or shaman?
Any of those classes can be viable. However, warlock and shaman are doing better at tournaments, with shaman having the edge. But, those are very specific builds of each class. That doesn't make the class inherently better or worse.
The hands of a healer