Of course dumping stuff to the command window will slow things down. That forces MATLAB to format your variables for display. Plus, it forces MATLAB to scroll the command window. How would you not expect it to slow things down? Everything you do that takes away from actual computations will always slow the calculations down.
The point is, if you want fast code, then DON'T dump everything out.
At most, display information rarely, only what will be useful, perhaps to show that your code is working to your satisfaction.
Learn to use waitbars when that will help.
It is often useful to display information not every iteration, but perhaps every 100th iteration, etc.
Garrulous display is a killer of efficient code, even if the code is well written otherwise.
In my codes, I sometimes have used a multi-level display flag. Thus if I am debugging code, I want an in-depth display of information. But normal usage requires less information displayed. And when I know things are working perfectly, I allow all display to be turned off.
