L2Ds were flying out of near-by Clark Air Base during WWII. There's reports of several Japanese aircraft shot down into Subic Bay... it's likely that an L2D could have been one of them.
C-47s also flew in the area, but only 2 remain unaccounted for in this area, that I can see. One shouldn't have been anywhere near Subic. Another may have (dropping supplies on nearby Bataan Peninsula), but I've not found any reports of an Allied aircraft being downed in the Bay. Several PBY's were strafed and sunk by the Japanese during the invasion, but these were in a known location, not near where we found this wreck.
I've not heard of any Li-2 flying in the area, either during or after the war... although many C-47s and variants did end up in civil aviation use post-war. Having trawled various databases online, I can't find any reference to a C-46 or variant crashing in the Bay post-war though...
So, the L2D is definitely the most 'obvious suspect'...