I smoked a bunch of habs for my last sauce. Cut them in half, smoked them with pecan for 1 hour, and still have plenty of smokey flavor in the finished sauce after fermenting and cooking...
Yes smoking darkens peppers, but it also depends how long their in the smoker and how much wood is smoldering. I have a zip bag of some blackened caribbean red's that don't take much of to heat or smoke up a dish, and I have some slightly darkened red jalapenos that I reconstitute in water and cook in a pot of chili, outstanding...but just a side note, I partially de-hydrate first before smoking, that keeps my de-hydrator clean smelling for when I use it for fruits and vegis.
I smoked some datils with cherry wood for two hours while smoking a pork shoulder. Pulled them off and straight in to the dehydrator. Then ground them to a powder. They came out awesome and add great heat and smokiness to whatever I put it on.