The young men are accused burglarizing the home of an acquaintance and stealing the guns, including an AK-47 assault rifle, on May 4.
A 17-year-old Scotts Valley High student was also arrested, but he was not identified, because he is a minor.
Johnston pleaded not guilty to the burglary, and Estrada’s arraignment was postponed to allow him time to hire a lawyer.
Both are due back in court in Santa Cruz on Tuesday, June 1. Police said the case is still open, and the missing guns have not been found.