Ok, so it looks like Scrutinizer is jumping the gun a bit on those notices.

Basically, Twig wasn't happy with the API that they had for Twig_Function, so they're pushing everyone onto SimpleFunction for 2.0, which follows the new API, and immediately deprecated it. In Twig 3.0, they're going to bring back Twig_Function with the new API.

Technically the deprecation notice isn't wrong, but the current implementation is the recommended way of doing things, and will remain that way until Twig 2.0 comes out when we can use Twig_Function again. We physically cannot fix the issue right now because Twig_Function doesn't exist in 1.x anymore.