I would recommend avoiding branching a subset of a repository. If you find yourself really wanting to do that, it may be worth pondering if you really need to split things out into multiple repositories.
The branches themselves are made with cheap-copies, you consume no space on the server for each branch.
It's going to be confusing to manage which projects exist on which branch, as you noted it will also may be a hurdle for some of your team to have to figure out which revision of a missing project to copy in to 'branch' it. I'm pretty sure members of most teams I've worked on would just grab the latest - this may be desired, but conceptually that seems even more confusing to me.
It may also be a hurdle to see a diff between two branches - there will be a lot of forest, making it difficult to pick out the trees you actually wish to see.
It's definitively the community norm to branch the entire repo. I'm sure you could make it go - but your successors may curse you.