Hi, my brahmas have been cuddling up together overnight in the nesting box area of their house from their first night with me when they were 10 weeks old. I wasn't really worried about discouraging it until I read that there are some disadvantages...
1. If the nest box is soiled, the chances are the eggs will get dirty too, and possibly absorb bacteria
2. If any eggs are left in there overnight for any reason, ( like if you forget to collect one day)they are likely to be trampled and could get broken, which in turn could lead to chickens pecking and eating their own eggs(once started, difficult to stop)
3.apparently when chickens roost by sitting on the floor, their cloaca (vent) regularly comes into contact with droppings which is unhealthy and can lead to illness.
This is just what I've read, I don't have much experience yet, so anybody please correct me if I've got it all wrong! And obviously I realise yours are only chicks now but they grow up quick don't they!
Anyway I hope this helps: I found out one day quite by accident that they don't roost in the box if I put shredded paper in there instead of straw. It must be that it's not so comfy for their big fluffy behinds. So now I put straw as the bottom layer for warmth, and then a layer of shredded paper. They very rarely sit in there now.
Hope this was of some use.
All the best with your endeavour!