In the strictest sense, yes: there will be some losses when a frame deforms. However, in-frame losses should be extremely minimal, especially in metal frames that don't dampen much. Assuming significant losses happen, it's probably in the rider's leg due to kick-back. But this hasn't been well-quantified. And it's entirely possible that flexy cranks have some (possibly frequency-dependant) benefits with respect to smoothing motion and biomechanics. The point is, there haven't been detailed, rigorous results in any direction. Considering that people don't seem to actually seem to suffer on flexy frames, and that the big manufacturers haven't published anything on the matter despite screaming about the benefits of stiffness for the last several decades, it seems likely that ultra-stiff cranks have very minimal performance benefit if it exists at all.