Arthur, welcome to the forum! What a lovely waterpark you have down there in Australia. Best of all, it appears to be conveniently located and quite accessible for the community!
It is quite observant for you to notice the Serial # alteration. You weren't specific about the details, but if you are purchasing from a dealer and there is a choice (all other things being equal), I would avoid the suspect boat and choose another. But if that is a special deal one-of-a-kind, I presume it comes with a financial incentive. In that case, I would simply ask the dealer for a letter authenticating the alteration so when you sell it later, you'll have a good explanation for the new buyer.
If, on the other hand, you are buying from a private party, I would ask for that explanation. Further, I would write or e-mail to the local police department and inquire whether there have been any reports of stolen Hobie kayaks. If this were a "new" boat, it would almost certainly have been reported by the local dealer or known by Hobie Australasia. Keep a copy of this correspondence for your files. If there are no red flags, you should be able to buy the boat with peace of mind.
I inadvertanly bought a stolen bicycle once. The police depart verified that it was stolen and immediately suspected me as the thief. Fortunately I had documentation. They confiscated it anyway and I was able to re-purchase it later from the insurance company. Not the greatest deal as it turned out.
So I think you are wise to look into this!