Mr Antunovich said many family members were yet to be told of the charge against the youth, who will reappear in court on Friday.
The short-statured teenager was supported by several family members, one calling out "mama loves you'', another "take care, boy''.
Waipuka was remanded in custody without plea until December 21.
His lawyer, Rob Stevens, successfully argued that Waipuka's image should be suppressed but said his name had already been widely published so there was little to be gained in seeking name suppression.
Speaking outside court after the hearing, Detective Senior Sergeant Scott Miller said he hoped this initial resolution brought some comfort to Cottrell's family and colleagues.
He said the investigation was nowhere near the end.
"In fact, it's almost just beginning. We have a lot of work to do and we wish to carry on with that work.''
Police were not seeking anyone else over Cottrell's death but they still wanted to hear from anyone in the Boulcott Street area between 5.30am and 5.41am on Saturday, including a couple and a Wellington Combined taxi.
"We need information from members of the public, not just in the Boulcott Street area but any information on Saturday morning or the previous evening in relation to this case throughout the whole of Wellington city,'' Mr Miller said.
"I also believe that these two offenders would have spoken to their associates and there are people who know exactly what has gone on with information we may or may not have and we encourage them to speak to us.''
Cottrell's wallet was stolen in the attack, and Mr Miller said police had found a brown wallet during a search "in the Wellington area''.
Police had searched two Lower Hutt properties searched during the investigation, and were still at the properties.
Mr Miller did not believe Cottrell knew the teens charged with his murder and said he could not comment on whether they were known to the police, were before the courts on other matters, or if they had gang affiliations.
The 17-year-old's grandmother said outside the court that her mokopuna was just "a baby''.
"I'm so sorry about that man,'' she said, breaking down in tears.
"I'm so sorry for his family.''