I've had a moonroof on every vehicle I've owned since I've been chasing: one Jeep Cherokee and two Toyota 4Runners. I've had one moonroof glass pane broken: June 1, 2004 from dense baseball hail near Windthorst, Texas. In other instances of hail damage to my vehicles, the moonroof glass has held up perfectly. It's a sturdy pane.
When my glass broke on June 1, the excellent drainage system and the sliding headliner cover protected the interior of the truck from water damage.
It's a mixed bag about whether to recommend one or not. The problems involved with fixing or replacing them are huge. My moonroof still doesn't track exactly right from the 2004 damage, but it's not a big problem; I just have to hit the button a few more times to get it sealed flush.
It's pretty nice to throw back the headliner sliding door and get a perfect view of activity directly overhead, especially if you think that activity might be rotating.
As much as I hated waiting for the body shop to struggle while fixing mine last year, it was pretty cool yesterday to throw it open and see the underbelly of a supercell without having to lean forward and look up through the windshield. I'd probably get another one on my next ride.