The answer is yes, no...and maybe.
NO, if the gecko is choosing to be there, which can be seen at times with our Missy when she will climb up on a proferred hand and sit there for a time.
Yes, and/or maybe, if by "holding" you mean "restraining". Pam and I try not to do that unless it's an emergency. If the gecko is clearly unhappy about being held and is constantly (or even intermittently) trying to escape, it can't be a good thing. You know, sort of like those relationships where one party is abusing the other, but the abused party can't find the power to actually break free. It's not good for humans, and it can't be good for geckos.
The "maybe" part comes in when you have a gecko that seems unhappy to be held for a brief moment but then settles down and seems to accept the conditions you've set for it. How the animal will react internally to that situation is going to vary with the individual gecko just as it would with an individual person.
We try to put ourselves in the gecko's place, to think, "If the Jolly Green Giant had me in a locked building but picked me up a lot and did this to me, would I thrive...or not?"
In other words, reptile critters are people, too.