From looking at some of the style guide for web applications that are available, there is a distinction made between the visual (icons, colours, logos, etc) and UI (look and feel of user interface elements) style guides. There are some overlaps between the two since visual elements also form part of the UI, but in terms of the way content (e.g. labels, messages, fonts, etc) is presented on the UI, are there gaps that are not adequately addressed in the visual guide that needs to go into the UI style guide, or is a hybrid combination of the two best for web applications (not websites)?
What you call visual elements are really just the parts that are unique to one application vs. another. The logo, color scheme, and icons are most often unique elements that have to fit into, and often determine to an extent, the style of the website.
UI elements are just building blocks that can be used and which are expected to be well known to people using the application. So using them and a consistent feel between applications will make applications have a familiar feel even though they are unique. You see this in that iOS apps have a different feel to Android apps.
There seems to be little value in trying to draw a distinction between what the various parts of an app in terms of guides or HIGs. They are just guidelines to help an application feel familiar to people and follow similar interaction patterns. I think they are fine as they are now.