Flagyl has caused cancer in boas and pythons. I would definately not use this routinely.
The only time you should deworm a snake is if it tests positive for worms. All medications have side effects and this could show up in other ways. Low hatch rates, brittle eggs etc.
How your geckos or lizards are going to get worms beats me. Unless you are keeping them in outside cages and giving them pond water to drink I have no idea where the worms would be coming from.
Your vet thinks this is a good idea because he sells you the medication and he cannot think of a good reason why you should not treat the animals.
Research done many years ago by two german students showed that very few of our indigenous reptiles had internal parasites. They really had a problem to collect and identify parasites despite going through the whole Transvaal Museum collection of many thousands of reptiles.
It is easier to ask for forgiveness than permission.
Those who are afraid to ask are ashamed of learning.