Template overrides are great, but sometimes you have no choice but to take a component apart to get it to do what you want it to do. It's great that all the code is open and you are able to do that too. What's not great is when you hand over that site to someone else and then an update notification pops up, prompting the new owner to undo all your hard work and ultimately break the site.
Removing the update server information from an extension isn't hard, the problem is that if you do it after installing the extension, the update server information is also stored in the database, so removing it from the component will make no difference. The update notifications will still come.
Removing from an extension, you can open the xml file, scroll down to the bottom and look for some lines similar to these:
<updateservers> <server type="collection">http://update.joomlart.com/service/tracking/list.xml</server> </updateservers>
Deleting that before installing will stop anything from happening. Sometimes though you don't know you need to hack until after installation.
There are 3 tables in the database which are associated with updates:
Where you want to look is dependant on what you want to do. The update_sites table holds the urls of the places joomla needs to check, so you might just be able to wipe out the site and forget about it.
If however, you have multiple extensions from the same developer which use the same update url you would have to look at the extensions id and then find it in the update_sites_extensions table and remove the row which associates it with the update url.
As there is an 'enabled' colum in Joomla 3.0's update_sites table I would assume that it is some thing we will be able to control in the near future.
Interesting Reading: Googles Joomla Dev Group