There shouldn't be. Urine is a weak acid, as is the acetic acid found in vinegar—if the system had a problem with vinegar, it would probably have a similar issue with urine.
In fact, regular doses of vinegar may even extend the time between cleanings to remove sea water calcium carbonate buildup on the electrodes. Use ONLY distilled white vinegar, never cider or any other variety...a cupful once a week.
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