Protect will continue to have support for any product as long as the updates have a public download URL. Shavlik would still support scanning and deploying any updates released prior to the end of life.
If Microsoft approaches the EOL of 2003 Server like they did with XP, it's possible they may offer extended support contracts. Generally new updates during the extended support period are not publicly available, and to continue support of these via Shavlik would require the use of a custom XML. If it gets to that point for you would first need to have an extended support contract with Microsoft, and we would suggest you contact the Shavlik sales team to see about the possibility of custom support via Protect.
I hope that helps answer your questions.