How do I avoid update checks for third party software (cobook), dont want to "update" by mistake I have an app that I bought, unfortunately the company was also bought and the new version is seriously worse.

Hiding is not possible for third party software.
Removing MAS receipt makes the software "damaged".
Setting softwareupdate ignore cobook, does not work either.

There has to be some hack available, I don't want to "update" by mistake, and it bugs me to see the red "1", since I usually keep my software updated.

This would however be a downdate.
The MAS receipt is designed just so you can't do that - otherwise you could hand the app to all your friends without them having to buy it ;-)

Did you try telling App Store to "Ignore Updates" - right click in empty space to the right of the App name… though I've heard reports this is no longer working in Yosemite; I've no updates to test on right now.