I have a custom recovery (TWRP) on my Nexus 7 (I'd forgotten about it) but stock on my Nexus 4. Both received OTAs and installed without issue, but I have read of users having problems with non-stock recovery and OTAs. It probably depends on the exact version.
One important thing is not to modify the stock image in any way at all as changes in an app or build configuration can result in the OTA failing when it does its checks on the existing system prior to installation. Even just disabling (freezing) a system app can prevent the OTA from working, as I discovered the first time I tried to do a OTA on my Nexus 4. The Nexus 7 came later so I made sure it was truly stock - apart from forgetting about TWRP - and it worked first time.
In all cases it broke root, despite my use of "rootkeeper" mechanisms which I have now abandoned. It's just as easy(and more reliable) to let the OTA break root then re-root afterwards than it is to attempt to prevent it from breaking root in the first place.