We've got a fairly large university site on SPM, currently 10% into a conversion off of SP2013.
Determining a structure now... I've established about 15 hub sites (all communication sites), each having 3-9 dept sites (mix of Team and Comm sites) linked into that hub level menu. We utilize the Start page, as well as a Home page for the University...where there is a menu with links to each of the hub sites.
We want to benefit from Audience Targeting, but are torn whether
(A) to use a common global megamenu at the top level each hub, then set all the hubs Visitor permissions to 'Everyone except External Users'..which may over-saturate the Start page. It may also expose (perhaps) department level docs to outside divisions..which some see as undesirable.
(B) The alternative is to remove the global hub menu; give users access to ONLY their depts sites and div hubs...and rely on audience targeting to bubble up documents to the start page.
Removing the hub navigation, to me, takes away the desire to instill collaboration between areas of the university. Some though, want the security of only users seeing what you absolutely need to see.