The screenplay specifically says the dog is a drug-sniffing dog. Also, at the point where the dog notices Uhura and Chekov, they had just beamed in; nobody calls for an intruder alert until they notice the power drain, so the sailor and dog were just on a routine drug patrol.
Why do you want to use facts from the script when you can speculate and push your own theory?
Drug abuse by naval personal IS a thing. Random testing in 1982 showed 7+% of tested personal were positive for drugs.....
http://www.public.navy.mil/surfor/Pages/NotOnMyShipNotInMyNavy!COSetsHisSightsOnSpice.aspx
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