Best practices for SharePoint permission

Hi,

I just got an environment in SharePoint Online to manage in a small organization.

There are department sites but have many sharing links and granular permission on the items level since it is common that one department works on some files with one person from a different one.

How does it work in your organizations? Sharing links are allowed (and in consequence breaking permission inheritance)?
It becomes a nightmare to manage with so much granular permission but also need to understand the agility of the company and bring users what they need.
Any suggestion on how to organize it the best way taking into account the above?