In the past, it was a general expression of enthusiasm, like "Yow!" or "Yee haw!" It could be sincere. It was probably regional; when I hear it I think of the U.S. West and cowboys and rodeos.
In the 1950s, it was the subject of a hit popular song, "Hoop-Dee-Doo" (variant spelling of the same phrase).
Hoop-Dee-Doo, Hoop-Dee-Doo,
I hear a polka and my troubles are through;
Hoop-Dee-Dee, Hoop-Dee-Dee,
This kind of music is like heaven to me!
Hoop-Dee-Doo, Hoop-Dee-Doo,
Has got me higher than a kite--
Hand me down my soup-and-fish, I am gonna get my wish
Hoop-Dee-Doin' it tonight!
One version:
https://www.youtube.com/watch?v=YXtHyydM5Ac
In the song, it's sincere. It means "I love to polka and I am really excited to be going to a polka dance."
The expression... as well as polka music and the accordion... in U.S. culture have overtones of being old-fashioned, rusticated, unsophisticated. So nowadays it is more often heard in an ironic context. It's spoken with a mocking intonation and means "I am not enthusiastic about this at all."
"I just heard that Dunkin' Donuts has started offering pumpkin spice coffee again!"
"Well, whoop-tee-doo."
Or "I could care less."
Or "Big whoop."
In each case, meaning "I don't think this is exciting."