Odd. Do you not see bioluminescence on Laythe at all too? Or EVE cloud cover? Everything is linked so if you don't see clouds on Kerbin you won't see them elsewhere too. If you see clouds on EVE, then everything is working correct and there's just not any clouds above the KSC at the current moment.
In CKAN when you select Spectra, do any of the required components in the box at the bottom right show red text? If you're not seeing clouds it's possible that EVE is marked as out of date for the current KSP version, which means CKAN doesn't install it, which is the reason why you don't see clouds?
Also, what other visual mods do you have? If you install only Spectra, does the issue still persist?
Hey there creator of Spectra here, if you're having troubles installing it, I highly recommend using the CKAN mod loader. It greatly simplifies the installation process.
HafCoJoe's post in How do I make my game look like this and how to install spectra was marked as the answer