Additional coding would interfere with the future updates of vB. However with some careful guidance it should not affect it too much. For example if you modified your 2.2.9 and wanted to upgrade to 2.3.0 you can use the tutorial which can be found in our hacking hints and tips forum or simply follow the instructions about upgrading given in the members center and go back and re-apply any code changes.
No it does not break the license agreeement
You can still get support for your vBullein board here but at vBulletin.com they prefer to provide support for the code originally used in the software and not code that has been modified
Hope that answered your questions
All the best,
- Dean