Television footage showed the body of a man said to be that of Villegas lying in a pool of blood as policemen looked for explosives.
De La Cruz was reportedly unharmed when police entered the Halls of Justice.
Ramos had demanded a ransom of $62,000 from Ramos's family to spare the lives of the hostages.
After leaving military service, Villegas did odd-jobs including working as a movie stuntman.
An investigation would be conducted to determine how the suspects managed to smuggle weapons into the courtroom, Sigfrido Tinga, the mayor of Taguig district southeast of Manila, said.
The authorities had evacuated an elementary school nearby as a precaution.