Workbench is a third party application used to connect to your Salesforce org(Production/Sandbox) using SOAP/REST/Metadata/Bulk APIs.
Its not enabled for entire organization but per user basis. If a user logs into Workbench it won't get enabled for others users.
Just like above point, its enabled per user per organization. Its possible that one user from one sandbox used Workbench and the same user in another sandbox not used Workbench.
So while logging in you should select for which environment(Production/Sandbox) you are trying to log in. For best experience, first log in to environment(Production/Sandbox) and then login to Workbench so it can use the current sessionid and log you in to Workbench for that that specific Production/Sandbox.
In change migration perspective, there won't be any issues as it just uses your metadata and won't update your metadata.
Hope this helps to understand better.