No, these were actual U.S. releases with catalog numbers ending in 1 and ESRB ratings and everything. You're probably thinking of the B&W Neo Pocket games which came in clamshell cases and were released in the U.S. only through mail order and were the same as the versions released in Europe and Asia (except Japan).
The full list of games released in clamshells in the U.S. is:
Fatal Fury: 1st Contact
Bust-A-Move Pocket
Metal Slug: 1st Mission
King Of Fighters: R-2
Baseball Stars Color
Pocket Tennis Color
Samurai Shodown! 2
And probably the Dyna casino games, though I've never seen U.S clamshell versions of them personally. They were released at the same time as the above games and it's probably just because they sold so poorly that I've never seen U.S. clamshell versions.
I don't know so much about which ones were released in clamshells in Japan. The Best Collection games CosmicMonkey mentioned were, but so were the launch games, I just don't know the exact list.
All the above games as well as Neo Turf Masters, Crush Roller and Neo Geo Cup '98 Plus Color were released with special multi-language packaging for Europe as well as the English-only packaging released in Europe and Asia (except Japan).
The exciting world of Neo Geo Pocket Color package variants!
...word is bondage...