Nvidia Shield OTA Updates and Rerooting
Probably Not.

Android updates before Lollipop checked each system file and replaced them but after Lollipop, the updates check the whole system block as a part and update it. Since rooting modifies the system files, the System Block won't match and the update will abort.
Since you have a custom recovery, the update won't even go that far because you need Stock Recovery to install it.

TL;DR: Attempting to update won't brick your device; but why leave it to chance?
On the off chance you install stock recovery and proceed with the update and it works, yes, you would loose root. You can reroot the same way you did it before.