So the question is: which full-screen DS games use the gap between the screens as in-game playing area, and which simply pretend that it does not exist. The latter approach is of course the most sensible no matter how you look at the issue. For one thing, in the latter approach enemies can't hide there. For another, you can use emulation to play those games using a single screen, overcoming the hardware's limitations.
So this is a list thread, but be sure to also provide one screenshot that proves the point.
NO GAP (good games)
Windy x Windam
GAP (bad games)
Catch! Touch! Yoshi! / Yoshi Touch & Go
Contra 4 / Contra: Dual Spirits
Kage no Densetsu -The Legend of Kage 2- / The Legend of Kage 2
Windy x Windam
Contra 4 / Contra: Dual Spirits
Kage no Densetsu -The Legend of Kage 2- / The Legend of Kage 2
P.S. Note that most games do not use both screens as a continuous playing area, so they do not have this problem...