Martin Young, of Glenbawn Park, and James Bingham, of Causeway End Road, Lisburn, were treated in hospital for gunshot wounds to their legs.
They were expected before Newry Crown Court charged with supplying a Class A controlled drug in 2013.
The court was told the pair had been discharged on Thursday night.
The court heard that Mr Young and Mr Bingham, both aged 39, had left the Royal Victoria Hospital, where they were being treated, of their own accord.
A prosecution lawyer said: "Both had superficial wounds. Nothing which would have prevented them coming to court."
The court was also told that Mr Bingham had made an application for a change to his bail conditions, so that "he could have dinner with his wife and child before surrendering himself to the court and custody".
However, Mr Bingham was in the company of Mr Young when they were shot at about 20:45 GMT in Poleglass on Thursday evening - a breach of his bail conditions.
The defence said it was unclear what had happened.
Another man, Alan Gerrard, with an address in Liverpool, also did not attend court.
The Courts Service said arrest warrants have been issued for all three men.
A fourth man, Brian Stewart, of Wansbeck Road in Hull, England, was remanded in custody to appear again on 24 March.
Two men who were due to appear in court on Friday failed to show after they were shot in west Belfast the night before, a court has heard.