I have an account which I haven't been on in about 8 months. I always check it to see if it has been attacked. I now know for sure it has because the number of defences on the 'Unbreakable' achievement has gone up. For months it has been at 175, but today I checked and it was at 176. As it is a rushed TH7, I assume this number has not gone up in a while because most people win their attacks against it. Since I stopped playing on the account, the number of trophies has decreased by about 300, further proof that dead bases are not removed from the game.
Edit:
Look at the link below for an explanation of why everyone believes dead bases are removed, but in fact they aren't.
http://forum.supercell.net/showthread.php/900884-Matchmaking-Observations-by-Reav3R?highlight=Flag+matchmaking




