Toolbelt cleans out some core WordPress features for you. They're little things that aren't used by most sites. There's no harm in having them, but by removing them we:

1. Remove some of the html in the header.
2. Reduce the overhead of generating the content.

Personally, I like to remove the features since I don't use them. If you don't want to do this or need some of the features then feel free to disable the module.

• Remove Really Simple Discovery (RSD) links. They are used for automatic pingbacks.
• Remove the link to wlwmanifest.xml. This adds support for Windows Live Writer.
• Remove generator tag from RSS feeds.
• Remove the next and previous post links from the header.
• Remove the shortlink url from header.
• Remove WordPress generator version.
• Remove recent comments widget style.
• Remove emoji styles and script from header.
• Slow down the default heartbeat to 60 seconds.