How do I disable Bonjour visibility after Yosemite install?

There is no more com.apple.mDNSResponder.plist in OS X 10.10. The service that controls mDNSResponder is now discoverd. The plist file you are looking for is actually:

/System/Library/LaunchDaemons/com.apple.discoveryd.plist

You want to add --no-multicast to the ProgramArguments in that file.

    <key>ProgramArguments</key>
    <array>
            <string>/usr/libexec/discoveryd</string>
            <string>--udsocket</string>
            <string>standard</string>
            <string>--loglevel</string>
            <string>Basic</string>
            <string>--logclass</string>
            <string>Everything</string>
            <string>--logto</string>
            <string>asl</string>
    </array>

Becomes

    <key>ProgramArguments</key>
    <array>
            <string>/usr/libexec/discoveryd</string>
            <string>--udsocket</string>
            <string>standard</string>
            <string>--loglevel</string>
            <string>Basic</string>
            <string>--logclass</string>
            <string>Everything</string>
            <string>--logto</string>
            <string>asl</string>
            <string>--no-multicast</string>
    </array>

You'll want to be very careful when editing that file. You can also use this script to do it for you - https://raw.githubusercontent.com/MacMiniVault/Mac-Scripts/master/disablebonjour/disablebonjour.sh

in Yosemite 10.10.5 here, there is no discoveryd or ever any reference to it on the whole filesystem.

I always install the 'hide bonjour' prefpane however and tweak the living crap out of the OS and remove all cloud, game and social media apps, and the rest of the CPU / RAM killing privacy crud too.

The app 'Lingon' is helpful for cleaning up launchD too. There is a basic free version too - if you look around :)