Are they better for cooling than taking the fan out and positioning a larger sized quiet fan such as Nexus which blows over a much larger area of the video card?
Replacing with a 92mm fan attached straight onto the heatsink is usually a better way of cooling with less noise. I say 92mm and not 120mm as 120mm is too big for the card so you waste airflow over the side of the card.
Is there a risk that the larger fan won't cool the card enough?
If it spins too slowly, yes, this is a possibility. Monitor temperatures when making any change like this.
Controlling the speed of the fan can be the complicated bit. Running the fan running at 5V is sometimes enough. You can also find adaptors to fit a standard PWM fan to the graphics card fan header. Then the graphics card will control the speed of the fan.