The cradle does not interfere with use of the touchscreen. (ereadertech.com)
On PlayStation the game can be operated in a number of ways from standard button inputs to use of the touchscreen on the PS Vita version of the game. (playstationlifestyle.net)
For what it's worth, Apple also has patents detailing Macs that feature touchscreen displays and MacBooks making use of touchscreen technology. (bgr.com)