Yeah, Zeek 3 was the big transition from Bro to Zeek so there are still areas where not every single command or line of code has been transitioned over to using “zeek” instead of “bro.” My guess is the warnings will go away in future releases of Zeek. For now, it is nothing to worry about.
It's possible that a plugin you have installed from the package manager or manually contained a zeekctl/broctl plugin and hasn't been updated for Zeek 3.0 yet. Take a look in /usr/local/bro/lib/zeekctl/plugins to see what's there and if one of the plugins there is using BroControl. If you find something in there using the BroControl API you could then go and file a ticket with the plugin that is causing the issue!