This sounds like an interesting project! :)
I'm not aware of a general document or guideline covering this, but happy to share a few thoughts.
About schema and security design on a HANA technical level please check the recent blog post https://blogs.sap.com/2016/03/29/hana-schema-user-and-role-security/ which I think provides a good overview.
The idea to provide each source system its own schema surely makes it easy to deal with the potentially overlapping namespaces but adds quite a bit of administrative burden to it. Which user is going to own these schemas? Ideally. this should be a single administrative account.
On the package organisation around the departments... I would strongly suggest reconsidering this. Solutions easily can stretch cross department borders and the responsible departments for any given function might/will change. My gut feel here is that it would likely be better to organise the packages around specific solutions and rather set up the necessary roles for privilege management.
Given the large number of source systems I also suggest to build the tooling for the management of the schemas and the roles/role assignments up front.
That's my 2cts on this.
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