The five medals match the efforts of Melbourne in 2012, Cali in 2014 and Paris a year later.
One night of finals remain, in which New Zealand will have interests in the men's 1000m time trial, the women's keirin and points race.
Gate, 26, had just five track sessions going into the worlds after mostly road racing for his new professional outfit, Aqua Blue Sport.
"I wasn't really sure what to expect coming into the competition as it was the first time it had been run under this format at the world championships," Gate said.
"I have had a blank canvas after Rio back working with my personal coach Simon Finnel and he has got me to this level.
''I've taken a completely different approach and so to come here off only five track sessions and get a silver is a credit to the work that Simon has done behind the scenes and the team at Cycling New Zealand."
Gate was sixth in the scratch race, won the tempo race but slipped up finishing 10th in the elimination race.
But he managed a cracking 40km points race only to have Thomas pip him on the final sprint on the last lap to pinch the overall title, Thomas finishing third and Gate fourth.
"I was keen to give it a nudge and race as hard and honestly as I could. That was good enough for silver on the day but gold would have been nice.
''Hopefully I can come back in the future and get the rainbows again," Gate said.
"It's been great to jump back in with the team. It's cool to see the team pursuit guys come away with a medal and I am sure they are as hungry as me to keep chasing gold and look ahead to Tokyo as well."
Mitchell has tended to be overshadowed in individual sprinting by his team gold team mates Eddie Dawkins and Sam Webster.
However those two were eliminated in the individual sprint quarter-finals as Mitchell saw off Australian Matthew Glaetzer 2-1.
In the bronze rideoff, Mitchell saw off Owens with room to spare.
Coach Anthony Peden has worked closely with Mitchell over the last 18 months to develop his one-lap speed and his sprinting ability, which finally blossomed when he was second in qualifying at the final World Cup in Los Angeles.
Mitchell had qualified fourth fastest in a personal best performance. But eventual champion Denis Dmitrov of Russia beat him in the semifinals. Still, a place in New Zealand cycling history was still there for the Aucklander.
"As for making history, our whole sprint squad is going really well and it could have been any one of us tonight," said Mitchell.
"I'm pretty new to the whole sprinting thing. I am fortunate to have mentors like Sam and Eddie, Anthony and the coaching staff to pave the way really."
In other action Jaime Nielsen finished sixth in the women's individual pursuit in 3min 31.653s, with Kirstie James 14th in 3:36.250. American Chloe Dygert was the class of the field, dominating the competition.
Sprinter Natasha Hansen finished 12th in the 500m time trial in 34.375, won by former junior world champion Daria Schmeleva of Russia in 33.282.
The pairing of Racquel Sheath and Michaela Drummond finished powerfully to place fourth in the women's Madison, after grabbing points in four of the last five sprints to overtake Italy. Belgium won from Great Britain and Australia.
