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Heck, you don't even *have* to block the nests - just go out at "bedtime" and physically move them from the nest box and onto a roost (maybe easier said than done given the coop design, I know). Generally, when they are ready to settle in if they are moved they just hunker right back down.

Coop design is causing the nest boxes to be the preferable roosting location.

To the bolded - not accurate. There are, however, other things that may be causing their preference - a little more information will help us sort that out for you. How is your coop set up? What is the height of the nest boxes and the roosts? Can you post photos of the interior? What are you...