Saw a documentary about that sub a few days ago. Apparently it did suffer a direct hit from the US destroyer, and went right down. They found the wreck recently at the bottom of the bay, with a hole on the side of the fin. Perhaps if the hit had caused it to surface instead of sinking it outright, it would have caused more than the emission of a coded radio message that got lost on the way up the chain of command, and people would have known something was up. At the very least the alert level would have been moved up a notch, and the radar operators would have been more suspicious of those planes that showed up on their screens. Just an uneducated guess though, as I'm no expert on military history.
Given the number of spurious sub sightings in the days immediately prior, you'd have to have it surface under attack & have numerous eyewitnesses (preferably a pic or 2, too...) to swear it's nothing like USN has. Then you'd have to wake the DO

(believe it or not, he was asleep...), & convince him to call up the chain & get Kimmel out of bed. Then Kimmel'd have to call Short, persuade him it's not a prank (or an unscheduled exercise, which they'd been having for a week or so, which also explains the phantom subs...), & get Short to sound GQ & AUS's
top alert status (not just a sabotage alert...), which (unfortunately

) means he has to violate his directive from DC not to alarm the public... By the time you've accomplished this, you maybe have a couple of hours to push the P-36s & P-40s into revetments, fly the PBYs, get AA guns & ammo ready, recall ships crews (from bars all over Honolulu...many in a state of falling-down drunkenness, indubitably), get WT doors shut (& some steam up for ship's power; hopefully, not enough to even consider an actual sortie

).
Then, when word comes from Opana Point, Hawaiian AF scrambles a couple of dozen P-40s, which are slaughtered by Zekes whose pilots have got years of time in type, & combat experience, to boot. USN loses a couple of DDs in the harbor, a handful off the channel (with luck, none
in it...), maybe a CC or 2 off Hospital Point. Japanese bombing is a
little off as a result; a stray bomb hits the torpedo store.


(Christie & Fife KIA?

Naw, that's ASB. The war's liable to be shorter, tho.) Kimmel sends word to Halsey they've detected an IJN TF to the NW. Halsey charges in;
Enterprise is sunk along with 2 CCs & 4 DDs in her escort. (With any luck, the stupid SOB would drown, but that's asking for a lot... Killed by a stray bomb fragment?

)
Next day, FDR calls it "a day which will live in infamy" (& doesn't get misquoted for the rest of time

). Kimmel orders the relief of Wake Island. Wils Brown leads
Lex &
Sara into the Battle of the Philippine Sea, sinking
Sōryū &
Hiryū. (
Nautilus is sunk by IJN DDs.) Japan surrenders in...hmm, July '44?