I've recently started a crusade to slay and recover the masks of all the Dragon Priests (Just the ones in Skyrim, I will deal with Miraak and the ones in Solsthiem in due time) and had a question. And the question is whether or not wearing one of the said masks will mess up the "Matching Set" perks in the Heavy and Light Armor trees? There's one or two I'd actually want to wear but I don't want to ruin the increased armor I'd get.

I'm going to say no, as there is a mod that fixes the issue if you're on the pc:

http://steamcommunity.com/sharedfiles/filedetails/?id=75861722

I haven't used the mod but I may give it a try myself.

If you're playing on a console, I'd say it probably won't matter once your smithing is high enough. The armor cap is 567 and it doesn't take long before most armor surpasses that.