Well, it depends ...
If the S1000R has a constant-mesh transmission (unlikely), then clutchless shifting isn't doing it any good.
If it has a synchromesh transmission (likely), then clutchless shifting isn't doing it any great harm.
The only damage (that I know) that clutchless shifting on a synchromesh transmission causes is an increase in the stress levels imparted into the transmission. Will that cause an early failure ... who knows. My guess would be that because the S1000R was essentially designed as a racing bike, the transmission is likely seriously robust, so ...