It sounds like they needed to do some serious energy cleansing of the area, and also you are very sensitive to either energies or emotional stress or whatever -without feeling it myself I can't give you a hard and fast explanation because it could be a number of things.
For instance the shop may be struggling financially and the stress had come to a head with a row or 'serious discussion' taking place not long before you entered.
The most likely explanation to me is that often if the shop is the centre of a very busy pagan scene with people coming in for friendship and socialising besides buying their supplies, OR if the place offers readings, healing or counselling of any sort something very serious may have come out in a session that was either still being discussed somewhere on the premesis or had happened very recently. In the way that often people can sense when a very big row or emotional turmoil has happened in a room in a house this kind of thing can effect the immediate area.
A reader cannot just stop what he or she is doing as they need to focus and help the person in distress, and the shop staff could have been dealing with customers, or just not been as sensitive as you are.
Chances are they hadn't got around to cleansing the area and shop (which should happen regularly for two counts, firstly you are getting every tom dick and harry through the door and the items they are selling are items that work on an energy level and hence should be cleansed regularly, secondly for the very reasons of the readings I mention above)
Should you feel the need the shop people may be interested to hear your tale and while counselling/healing/reading sessions are confidential they may be able to offer you some explanation.
The other explanation is that the person above me may also be correct in that these shops are forever burning incense, and some of them can contain odd ingredients, while I've never heard of full body aching being a sign of allergy who's to say that you are not allergic or at least sensitive healthwise to one of the ingredients. I'd go back again and see if the same thing happens :)