Rooting will not block any app updates and yes you will receive the JB updates, but as a rule I protect root with OTA RootKeeper from Google Play, as OTA's can remove root. As for custom ROM's, I use them to remove bloatware and give my device a facelift as it ages, but I do not find the Nexus 7 overloaded with bloatware and it still feels new to me. I may explore some of the custom ROM's as they reach maturity, but right now I plan to utilize the advantages of root and stay with JB.