The popular songs you know and love has all sorts of (copy)rights attached. To have it playable in Taiko, the Team has to only (hold various negotiations to) borrow the rights from their owners. With the deals comes all sorts of conditions, and for some the loan has to end some time, hence the removals.
The Team is sorry that some of the most memorable songs has to be removed one time or another. But rest assured they will be trying their hardest to get new and exciting songs into the games to add to that great memory hopefully.
本日午前中公開の開発日記にて太鼓の達人キミドリVer.からサヨナラとなる楽曲を発表しました。皆さんが知っている「アノ曲」は、それぞれ「権利」をお持ちの方がいらっしゃいます。我々はその権利をお借りして(のために色々とご相談して)みなさんに遊んでいただけるようになっています。(つづく
— 太鼓チーム (@taiko_team) October 9, 2014
権利をお借りするには様々条件があり、サヨナラとなってしまうことはそれも1つお約束なのです。皆さんのそれぞれ思い入れのある曲が遊べなくなってしまうことは我々としても残念ではありますが、また新たな思い入れをもってもらえるよう今後も努力していくことで代えさせていただければと思います。
— 太鼓チーム (@taiko_team) October 9, 2014
So there. The Taiko Team doesn't hate you with the removals. If they hate you they would have start mass-removing Namco Originals like Xa, that Namco holds most rights and has no decent reason. Speaking of Xa... (one more post today!)