I'm against them for a couple reasons.
1) A horse is designed to move. It's physiology works in such a way that constant movement keeps all body functions in top health. For example: a horse standing still for prolonged periods of time can suffer from loss of bone density, loss of muscle tone, poor circulation, accumulation of fluid in its legs ("stocking up"), etc.
2) A horse's psychological health requires a few things: ability to move (they are flight animals), ability to interact with other horses (even if this means just having a horse in view -- floor-to-ceiling walls definitely doesn't allow for this), and ideally something to think about or do (they're not stupid animals!). Standing still for the night doesn't meet any of these criteria.
Also, as Velvet mentioned, poor ventilation could be a problem, which could lead to respiratory issues.
Is there a reason you'd like them to be inside? A better solution might be to create a shelter for your horses and let them choose to come in when they'd like. You could always save the standing stalls for emergencies, like bad weather, or take down a couple walls and make a box stall or two for backup.