I found this slide (from Vesa Juvonen’s March 2018 PnP video on SharePoint Hub Sites video presentation) to be a good illustration of the new, modern direction for SharePoint site IA. It stresses a “flat-earth” approach for modern site collections… dispensing of site collection sub-sites in the name of O365 performance, and the flexibility and ease of making and breaking site associations between hubs and root-site site collections.
Notice the black-pentagons in the diagram… for those scenarios where “classic” site collections need sub-sites. I do think there remain scenarios for these until modern sites fill the gaps…. scenarios where search sites, record centers and departmental IA concerns (e.g. site collection specific site columns, Content Types, search, document sets, etc) are required.
Interestingly…. 2 hours after I published this, Microsoft released a Hub Planning Guide. After a quick read, I think many (but not all) of the ideas in the guide are reasonable. I’ll have more to say about this soon.