Does this only affect visitors to the site and not those that have logged in?
Strictly speaking: No (as a logged in user is still a visitor, so your statement "Does this only affect visitors to the site" is wrong).
This Add-on sets a default for those visitors that have not yet made their own choice (=guests without cookie).
A logged in user has already made a choice that is stored in his profile in the database.
It wouldn't make sense (or even work) to apply the default for logged in users.
Think about this scenario:
- Someone visits your forum for the first time.
His system is configured to prefer light but you have configured dark as default so he gets dark (without the Add-on he would get light)
- The visitor doesn't like dark and switches to light
- The visitor registers
- The visitor closes this browser (which is configured to delete all cookies on close)
- A few days later he comes back and again gets dark (as there are no cookies and you've configured dark as default)
- The user is already somewhat annoyed about getting dark agai and logs in immediately, expecting to get his preference (light)
Would you still want your
default applied in this case?
If this was done, the user would never be able to set their own preference.
What you could do (though I'd strongly advise
not to do this as it might annoy users) is to update their preference:
The update changelog gave me the impression I can see the active style for each user
without the add-on installed (and before this update)
After this update:

Or via batch user update.