Louis Morton, in his work The Fall of the Philippines, indicated that it was a bungled notification on MacArthur's part led to Manila's bombing after the declaration was declared
To understand why, we must first put the events in order. On the 26th of December 1941, Manila was declared an open city, and all over the Philippines, radios announced as such. However, supporting testimony from radio announcer Don Bell (real name Clarence Alton Beliel) during the USA VS. Homma case suggests that MacArthur neglected to give the official announcement to the Japanese, and records from the same case mentioned that the Imperial General Headquarters in Tokyo didn't have the information up until the 27th of December and Homma's forces didn't have concrete proof that they knew up until the 31st of December.
However, the bombing of Manila did go on until Japanese forces entered the city on 1 January 1942, and thus Morton also posited that even if the Japanese forces under Homma did have the information by the 27th, they chose to ignore it, whether from doubt or from inconsideration we may never exactly know, the judgments from USA vs. Homma notwithstanding.
However, on the Japanese side, there is a justification that Col. Yoshio Nakajima, an intelligence officer and subordinate of Homma, used in the same USA vs. Homma case mentioned above. He mentioned that their information on Nichols Field, a military airfield smackdab in the middle of Manila which is now Ninoy Aquino Airport, indicated that it was still operational, and thus a valid military target, together with the Manila docks where military supply ships still park and acquire provisions for the forces setting up the defenses at Bataan. This was countered by the prosecution in the case that on the 28th of December, Japanese bombers hit the city of Intramuros, a place of cultural significance.
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