Loaiza was booked Friday on charges involving the possession, transport and sale of 20 kilograms (44 pounds) of suspected cocaine.
His bail, initially set at $200,000, was reportedly increased to $250,000 on Wednesday because he was deemed a flight risk.
If convicted on all counts, Loaiza faces more than 20 years in prison. Deaton as well as Loaiza's relatives left the courtroom without speaking to reporters, and the attorney did not immediately return phone calls seeking comment.
Loaiza is the second-winningest pitcher from Mexico in major league history.
San Diego Sheriff's Department Lt. Jason Vickery told ABC News the drugs were found in Loaiza's garage hidden in duffel bags and were packaged in a way that they appeared to have been transported from Mexico to the US for distribution throughout the country.
Climber dies after fall on Mount Hood, rescuers reach others stranded
The climber fell into the Hogsback area , which is at an elevation of about 10,500 feet, at around 10:30 AM. Steve Rollins of Portland Mountain Rescue says Hogsback is the most popular climbing route on the mountain.
A search of Loaiza's vehicle revealed "a sophisticated aftermarket compartment used to hide contraband", the sheriff's department said. That provide enough probable cause for officers to seek a search warrant to take a look in his home, which he leased in early February.
Sheriff's Lt. Jason Vickery said the deputies had been surveilling Imperial Beach as part of a narcotics investigation and had spotted him in a 2010 Mercedes-Benz mid-size SUV believed to be linked to a smuggling operation. He last played in 2008 with the Chicago White Sox and Los Angeles Dodgers.
The former All-Star made $44 million in his career pitching for eight teams in 14 seasons.
She filed for divorce shortly before her death, ending their two-year marriage.
Loaiza was born in Tijuana and he attended Mar Vista High School in Imperial Beach.