Collecting SCM data during code analysis can unlock a number of SonarQube features:
code annotation (blame data) in the Code Viewer
SCM-driven detection of new code (to help with Fixing the Water Leak). Without SCM data, SonarQube determines new code using analysis dates (to timestamp modification of lines).
Turning it on/off
First of all SCM integration requires dedicated SCM Provider plugin(s) to be installed. See Plugin Library for more on that.
Then, if need be, you can toggle it off at global/project level via administration settings.