The evidence acquired by Graysmith that could implicate Allen was merely circumstantial in nature. Circumstantial evidence is insufficient to form an entire case or charges against an individual, as they can lead to one or more conclusions. Without additional physical evidence to corroborate a story provided by the circumstantial evidence, nothing can really be done as guilt can't be reasonably assigned.
Graysmith likely wanted Allen to know he believed he was the killer, but given he already lost his job and wife due to trying to uncover the killer to no avail, it's not very likely anyone would have listened to him at the time.
The intent of the scene is to simply show Graysmith still and will likely always believe Allen was the Zodiac killer, but ultimately leaves everything open for the viewer to interpret. Was Allen really guilty, or was Graysmith being driven insane by his obsession with the case?