Nintendo are shutting down the wifi because it cost money to have networks or online services. Since they aren't producing games for the older systems anymore, Nintendo are trying to promote their newer games. I think it makes sense to take away the wifi from older games, since not many people use the wifi in older games. The newer games have more players than the older games, and the newer game players would outnumber the players from older generations eventually.
Also, your other question-You will not be able to use the gts anymore when the wifi is shutdown. If you have a Pokemon deposited in the gts and you don't take it out before the wifi shuts down, you will never get the Pokemon back :( since it is locked on the gts.