Nothing that I'm aware of aside from your knowledge of what the site is using.
Keep in mind if the client or end user wants to change their license or start using features they weren't before and you haven't included that module, they have to go through and re-install it. This could cause problems if they don't have the KIM or access to an instance with their hotfix version. My experience has been the more you try to customize the base instance, the harder it makes it for the client to perform upgrades and such.