Simple, if the Spanish did not invade the Philippines, Northern Philippines would be a Bruneian territory and we might still have independent states in Mindanao and Sulu. This is what I think if the Spanish did not invade the Philippines, the three dialect Groups; North Cordilleran(Cagayan Valley langauges), Central Luzon and Sambalic would have merged into a single linguistic unit or to simplify it they would have merged into one language or language community due to their similarity and later they could overwhelm the other linguistic groups in the northern Philippines, the decimation of population and resettlement in those areas prevented this from happening. I know this would happen after I researched and found similarities which would cause these linguistic entities to merge with each other, another is that the Bruneians would retain the Northern Philippines as their territory and fief until the people of Northern Philippines or Selurong rebel or the Bruneian Empire falls for another reason but I think the Sultanates of Sulu and Maguindanao will survive but if the Bruneian Empire targets these states they will also cease to exist as independent states but I think Sulu will cease to exist because Brunei is trying to annex it as well.
So yeah, it is not really a question of the Philippines is discovered or conquered or not but a more interesting question is if the Bruneian Empire did not exist because if the Bruneian Empire did not exist.
If the Bruneian Empire did not exist, Luzon will remain under the control of the Tondo Dynasty, who are secretive and isolationist and I don't think they will have Manila as a capital, they will shift the capital to a more secure one presumably in OTL Region II or Region III because Metro Manila is easier to be attacked so it will be important in trade as well as the Zambales-Bataan coast, they wil remain pagan and become more buddhist because they will be more attracted to the Sinosphere and Japanese trade unless they have more ties with the southern neighbors which will lead them to Islam. Another is about the Sultanate of Sulu, the Sultanate of Sulu will exist and become a trading hub in the OTL Philippine Sea, it maybe doubtful if the Sultanate of Maguindanao will exist because the Sultanate of Sulu might expand to Maguindanao and Visayas. If the Bruneian Empire did not exist if the Spanish still discover the Philippines they will not be able to conquer Luzon and Mindanao because the dynasties controling those areas will be more stable than OTL and are immune to the Smallpox.