By 1960, 4 of the five were found. But, without the 5th one (which turned out to be the one sunk by the USS Ward) there was room for speculation.
Finally, the one sunk by Ward was located.
One sunk by Ward.
One sunk around 0830 on 12/7/41 by USS Monaghan DD-354 just inside the harbor.
One found in the defensive zone outside the harbor in 1960 with both torpedoes aboard.
One ended up drifting, and was captured.
Leaving the so-called "three piece" sub, first found in 1951 blown in half in the defensive zone outside the harbor, then forgotten about, then found again in 1992, and surveyed periodically from then on.
That sub showed damage from its scuttle charges, and its torpedoes were gone. It also showed evidence of having been salvaged and cut up.
After the one sunk by Ward was located, now accounting for them all, a theory developed from an aerial photo of the attack, radio transmissions from one of the subs claiming success, and the fact the sub showed signs of salvage work.
That theory was that it penetrated the harbor, and fired its 2 torpedoes at West Virginia and Oklahoma, then went and hid in the West Loch of the harbor, broadcasting the success signal. Unable to escape, the crew then set off the scuttle charges. In 1944, an ammunition accident in the West Loch sank a number of landing craft which were dredged up, and removed, being dumped outside the harbor. It was thought this sub came up with this. It did account for all the factors...missing torpedoes, scuttle charge damage, and salvage damage.
However, in 2013, another theory came out. A report was found by USS Saint Louis of being fired upon with torpedoes as it left the harbor. Also, the report claimed that the sub found in 1951 had been cut up/salvaged/moved. It now appears this is the most likely probability.
The sub sat outside the harbor to ambush anything coming out. It fired at the cruiser, hit a reef, possibly thought it had hit the ship and radioed success, then scuttled itself. Then was further cut up and moved by the Navy in 1951.