I agree LE may not have known about Magnolia on Day One but with due diligence would have have known long before the Shell Harbor search over a year after the crime. IOW, in time to search and retrieve evidence if any was there, IMO.
I remember the conversation where Tommy told Lisa of the search being conducted at Shell Harbor dock and surrounding area. I do not recall him saying the Magnolia home itself was being searched, only that the search area was such that the entire area was off limits to spectators to the point where there was no access to their former home. I think Lisa was surprised to hear the search was vast enough to make Magnolia Lane temporarily inaccessible to the public.
JMO, and I could be wrong.
I too remember much of the the conversation to be as you have stated...JMHO