Personally I think bunnies (in fact all animals) are happier overall if they can be handled without stress, probably because I'm from a horsey background where they have to be amenable to anything you might want to do with them otherwise they are likely to be pts (yes this does happen, I used to work on a yard which was a last chance for a lot of horses and ponies in this position).
So. When we got Martha she was very scared of being picked up. She was from P@H adoption and was approx 4-5. We don't know if she had been handled at all in her previous home but doubt it. If she had then it was all undone by being in P@H. Before we took her home they wanted to clean her bum (which they hadn't previously noticed was dirty in the week that she'd been there :evil: But that's another story!) and it took 5 of them to hold her down (which certainly traumatised her more). When we got her home we discovered she loved snuggles and would sit on your knee for hours for noserubs, but she hated being picked up (I have the scars to prove it!). She also used to dig and nib at us if we stopped stroking her. So we ignored both struggling when being picked up and the digging/nipping. We picked her up anyway, gently and safely and keeping her secure at all times. After about two weeks she was far improved. After 2 months you could pick her up, carry her, put her down, with no fuss. Now she is relaxed with all handling as long as she is picked up and held in a way that makes her feel secure (ie fully supported and she prefers horizontal to vertical). Sometimes she doesn't want to be picked up and will move away. If we need to pick her up we will and she accepts this and is relaxed. If we just wanted snuggles then we leave her until she does too.
When we got Bugsy, also from P@H, they told us she was aggressive to people and had ripped an artery on one of the staff's hands. Later it turned out they were sexing her at the time so I'm not surprised she was kicking! And she had needle claws, which we clipped almost immediately in about an hour with minimal fuss. She was much much better than Martha to be picked up, almost no problems there (though she did give me a matching scar to Martha's one on one of the first occassions!) and now is also completely relaxed with all handling as we have taken the same approach that negative behaviour is not rewarded but being picked up and behaving in a relaxed manner (certainly in the beginning when we were picking them up as often as possible) is likely to get you popped back down and if not lots of snuggles.
Chestnut is currently getting picked up lots :lol: (even though he is very good and loves snuggles already)
I really think this approach helps when they need their nails clipped (I do it myself with bunny sat tummy up on my knee - Bugsy even spreads her toes helpfully!) or meds, as they know that any position you have to put them in is safe so they can relax.