But the 26-year-old Dunedin cyclist believes the New Zealand team will only get better.
The trio of Shanks, Jamie Neilsen and Lauren Ellis pushed the defending world champion British team hard, clocking a national record time of 3min 23.993sec.
Britain claimed the gold medal in a time of 3min 22.720sec.
But it was a stunning ride from a New Zealand team that has been together for only about six weeks.
"It's great to be back on the podium but we went out there to race for the gold medal, so that was a little bit disappointing," Shanks told the Otago Daily Times.
"But you've got to look at the bigger picture and we did a PB [personal best] time and really fought for the title.
"It was a great race between us and the British."
Shanks, who switched from netball to cycling four years ago, believes Bike NZ's Power to the Podium programme to identify athletes from other codes will continue to play dividends.
"Jamie Neilsen is from the Power to the Podium programme. She's only been riding a track bike [since December] ... and has picked it up so quickly and been willing to learn and listen to advice."
As far as the team's potential is concerned, Shanks was confident the team would continue to improve.
"We're still going places and this has been a pretty wicked achievement in the overall scheme of things.
"We don't quite know what the limits and boundaries are yet and we are still just finding our way.
"But as long as we can keep going faster and faster in each event then we are going to be good."
The silver was New Zealand's second medal at the championships.
Shanks won a gold medal in the women's 3000m individual pursuit on Thursday morning [New Zealand time].
She will be back in Dunedin soon and will take a break from the bike for the next six weeks or so.
She does not have any firm plans when she will return to the saddle but expects in will be some time in mid May.
"I'm having some down time to refresh the body and the mind," she said.
"I'm looking forward to coming home and catching up with family and friends, and chilling out and having a few glasses of red wine."
World Cup winner Jesse Sergent showed some inexperience by going out too fast in qualifying for the 4000m individual pursuit and faded over the final kilometre to finish with the fifth-fastest time of 4min 21.253sec, more than 3sec outside his winning time at the Beijing World Cup.
"I just went out just too fast and then got bogged down trying to get back on pace," Sergent said in a press release.
"At around 2km I was counting down the laps knowing I had just not got the early phase of the race right.
"A real experience for me, and one I will really learn from."
World omnium champion Hayden Godfrey had an impressive ride to finish eighth in the men's 15km scratch race.
Manawatu rider Simon Van Velthooven did not qualify in the men's keirin.
Auckland's Kaytee Boyd, another of the track converts from the Power to Podium programme, will compete in the women's omnium today, while Invercargill's Eddie Dawkins and Van Velthooven will take part in the men's sprint.
