Could Spain's heavy ships have changed either decisive battle?

Could Pelayo and Emperor Carlos V have changed the outcomes at Manila Bay or Santiago?

At Manila Bay, yes, if they had arrived fully worked up and in working order. At Santiago, the odds would still have favored the Americans.

At Manila Bay, Pelayo and Emperor Carlos V could have been dangerous opponents if available, fully worked up, and in sound working order. Their readiness and command would determine how much their greater strength mattered. In the same condition as the rest of Montojo's squadron, they would have shared its destruction. Joining Cervera at Santiago was a different proposition: even with those reinforcements, the odds would still have favored the American force.