So SCL determines the speed at which data is sent/received but some devices are not tolerant of a slower than expected clock?
What chip does the Nunchuck use?
There is not something like "the Nunchuck". Multiple vendors are using different hardware to build their own Nunchuck and all follow the interface definition.
You should always design against the defined interface and not against a specific implementation (e.g. the original Nunchuck from Sony).
When you want to avoid changing the standard library files, you can just set the TWI speed using the following code (copied from my posting at http://www.windmeadow.com/node/42#comment-28
#define TWI_FREQ_NUNCHUCK 400000L
TWBR = ((CPU_FREQ / TWI_FREQ_NUNCHUCK) - 16) / 2;
Is there any reason, why you want to avoid changing the speed? When there are other TWI devices which need lower TWI speeds you could try to switch the speed before accessing each of the devices.