Yes, a protein skimmer will increase evaporation because of the increased surface area created by the bubbles. More evaporation is GOOD in reef tanks because it aids in gas exchange and temperature regulation. You will find that your pH will fall and your temperature will rise if you purposely prevent evaporation. Furthermore, if you are using kalk then more evaporation means you can add more kalk.
I agree with the others with the NO2, NO3 spike being caused by the canister. Get rid of it. It is not required and will usually do more harm than good.
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