The Japanese would have little interest in the Philippines. Sure, they have some resources, but none that the Japanese particularly need (they have all the timber/grain/etc. they want in occupied China. The OTL Philippines Campaign lasted for months and then the islands saw significant guerrilla resistance until the Americans recaptured them. That's far too much effort to seize some islands that don't provide the resources Japan really needs (oil). OTL they invaded to prevent the US from having a major base right across their supply lines to the Dutch East Indies and British territories (which is what they really cared about). Here, they'll be happy to let the Philippines remain as whatever they are (either independent or Spanish).
As for how the US would respond to all this? American interests in Asia were always far more concerned with China; indeed, the main reason for the original American annexation of the Philippines was to secure a local fleet base for the forces they already had deployed to protect their interests in Asia. It's worth remembering that the Battle of Manila Bay wasn't the result of some American task force steaming from California on an expedition. The battle was fought by American naval forces already in China; in other words, the US already had a stronger fleet in East Asia than Spain did, despite not owning any land (the Asiatic Squadron being based at various Chinese ports prior to capturing Manila). Even without the Philippines this trade would continue, and the US would continue to oppose Japanese aggression against China, leading to sanctions (again, mainly driven by American pressure; neither the British nor the Dutch particularly cared, but went along to make the US happy) and probably eventually war.
As for whether the Spanish could hold the Philippines? I'm not qualified to judge, but it wouldn't surprise me to see a Cuba-like situation: frequent rebellions that get defeated by a combination of military action and selective buying off of elites, only to flare up again a decade later. The then-ongoing Philippine rebellion wasn't invincible, after all; the US defeated it after the war, and the Spanish had mostly pacified it before the Spanish-American War broke their control over the area (remember that Aguinaldo was in exile in Hong Kong until Dewey brought him back after Manila Bay). It's not like colonial rebellions in their holdings were a new thing for the Spanish, after all.