Mostly ease of administration. If you already have an active directory, your users already have an account and a password and a policy for changing those passwords regularly in place. So why make them remember another login and password? It's also easier to deal with users leaving your company. Just lock their Windows account and their LF access is also revoked.

If you have multiple repositories, LF accounts need to be set as named users for each repository, where a Windows account only needs to be set as named user per server.

For LF Rio, where the License Manager deals with named users, Windows users can be automatically synchronized with active directory. So just creating a domain account for a new employee and putting them in the right Windows group will  give them the correct access to LF without any extra work.

For Workflow purposes, Windows users are easier to use too since WF can read their email address and other properties (such as first, last name, title or manager) directly from Active Directory. Laserfiche users have to be individually configured with an email and other properties.

If you started with Laserfiche prior to LF7, LF accounts were the only option for authentication. There is nothing inherently wrong with that setup.