Because if they did integrate it, two things would happen.
1) Because the accessory utilizes the IR port on the 3DS, it would permanently disable the IR port functionality because Nintendo would place the IR transmitter and transceiver internally to allow the second circle pad to function.
2) Nintendo would integrate the second circle pad functionality internally so that it uses internal hardware similarly to the original circle pad (i.e., no IR sensor) but is no longer compatible with any game that supported the original Circle Pad Pro.
You can't have both. Either you implement the hardware absolutely identically (so old games keep working) or you change it (and no game continues working--future support only).