Yes, they are intimidated by the older chickens. This is normal.
You are doing them no favors by allowing them to get into a bad habit of sleeping in the nest boxes. Close off the boxes each night before roosting time. It's much more difficult to break chickens of a bad habit than to prevent them from developing it in the first place.
You can help your chicks learn to roost by providing them a safe space on the perch away from the older girls. You can do this by moving the youngsters to one end far from the older chickens or by adding a perch. A perch higher than the older perch will be very attractive to the young ones.
If space is a problem, you can provide safety for the chicks to roost by putting a partition on the perch so the older ones can't bother the young ones. I recently did this for a single chick I have that was just learning to roost. It can make all the difference.
Place your chicks on the perch close together for security and hold your hand lightly on their backs until they calm down. Touching their head with a light downward pressure will help them further calm down and get into the mood to sleep. Making "shhing" noises further quiets and calms and soothes. They will be roosting on their own in a matter of just a couple nights of this.