Maybe. But KGDB and friends do exist too in Linux. And (AFAIK) not everyone likes using those, some just like throwing a few printks here and there. That is not universal obviously :) My point is that yes, unikernels may not be as easy to debug etc at this point as regular usermode code, but it is something that can be worked around and I think if people begin to use them in-mass frameworks and solutions will emerge.
And you will want a mechanism to iterate quickly to see effects of tweaks.
Eventually you have built an interactive debugger.