Yes. With the merged profile and the cabinet off, you're using a direct profile of the amp and it is the most accurate amp profile with the cab off.
When you turn the cabinet off on a studio profile (as mentioned above by paults) the Kemper makes an approximation of what part of the profile is the cabinet is. Honestly, it's fairly close to perfect, but NEVER 100%. It will always sound different than the direct profile with no cabinet, in my opinion.
Now where it gets really interesting is when you play a merged profile with the cabinet 'on' through full range speakers or direct to recording. The merged profile is created by copying the cabinet module from a studio profile (and using Kemper's software approximation to decide what part to copy) and then pasting it to a direct profile and combining both. The merged profiles can be great for live use, but won't ever sound as good as a pure studio profile in my opinion. Again, the algorithm used by Kemper to approximate the cab is close to perfect, but not 100%, so the merged profile (direct profile plus cabinet) never sounds quite the same as the original studio profile in which the merged profile was created from.
So to answer your question again, yes, there's a difference.
For the most accurate profile without a cabinet module (to be played through a guitar cabinet with a clean power amp), use a direct profile or a merged profile with the cabinet off.