"If you want the IPL and two or three or four other tournaments as well, you probably can't have everything and that's a decision you've got to make at the start of the year and I just think the flexi contracts just make it a bit untidy," Hesson said on Sky Sports.
"It just gets really untidy when you've got 20 contracts or however many is on that [NZC] list now and then you have an extra one [for Boult] and next year you might have three extra ones and."
Boult, who last played for New Zealand during the 2022 T20 World Cup in Australia, is in line to be a part of the national squad for the ODI World Cup in India later this year.
With T20 leagues mushrooming across the world, Hesson feels NZC would soon face a situation where it will have to offer different contracts to different cricketers depending on their circumstances.
"Under the current model it doesn't. You get ranked in three different forms and you add the points up and that's your number and everyone has known that and it's actually worked pretty well for an extended period of time," Hesson said.
"This flexi contract, it might work really well for Trent and it might actually work well for New Zealand Cricket, but it does open up a whole can of worms."
"He'd [Boult] had a wonderful career for New Zealand and been a great servant and now almost wants a little bit of a dollar each way."
Craig McMillan
"It seemed only 12 months ago Trent Boult was more than happy to make his decision to move away from international cricket and take the riches of the T20 franchises around the world and you couldn't bemoan him that," McMillan said.
"He'd had a wonderful career for New Zealand and been a great servant and now almost wants a little bit of a dollar each way. It's a difficult one. It doesn't sit overly well with me and I'm sure it doesn't sit with some of the other players within the setup who are doing the hard yards then have to move back [when they return]"