What I did find didn't really give me a definitive answer, but it did show people using the different spellings of 'Harbor' over a period of time from around 1890 through to 1940/50. More recently however it does feel the spelling has settled and standardised on the American spelling.
I visited the Victor Harbor Information Centre and asked the question about the spelling. They've obviously been asked the question many times before as they had an information page titled "Why is Victor Harbor spelt without the 'U'?"
According to the information page "All six (6) Harbors in South Australia are spelt without a 'u'." The harbours listed were: Outer Harbor, Franklin Harbor, Rosetta Harbor, Victor Harbor, Blanche Harbor and Yatala Habor.
The reason given for the spelling being, "It can be surmised from the above spelling of all South Australian Harbour's with the 'u' that it originated probably from a spelling error made by an early Surveyor General of South Australia." (Note the use of the possessive apostrophe is from the information page.)
Personally I'm not convinced that it was necessarily a spelling error. It is hard to guess why something was done in the past using our current frame of reference. The township name was gazetted in 1914 as the 'Municipal Town of Victor Harbor'. Once gazetted that would tend to become the norm for government use. Spelling error perhaps, or could it be spelling preference? Who really knows!
I also decided to check the six listed harbours and found interestingly using Google maps that some appeared to be spelt with 'our' but that it was easy to be confused. If checking the spelling it is best to use the South Australian State Gazetteer using the PlaceNames Online tool. All of the above spellings were confirmed using the Gazetteer. Also interesting is you'll find inconsistent spelling such as the 'Outer Harbour Post Office' where the spelling for the Post Office differs from the spelling for the location.
One of the features of Victor Harbor is Granite Rock which is a lovely walk across a walkway over the water. A plaque on the rocks dated 1924 had the spelling 'Victor Harbour'. I'm sure the spelling caused no end of discussion for locals of the time.
In the end perhaps we just need to consider the spelling of place names have a history and accept the spelling as correct, even if it does vary from the usual convention.
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