To make sure I understand, you have about 100 managers in Workfront. You have a request queue where people can submit a request, and you want that request to be routed to the appropriate manager (and the user submitting the request knows which manager to select (it's their own manager I assume).
What you've suggested, setting up a queue topic for each manager, and assigning a routing rule for each), I think is the way to go. I'm not sure what you mean by "various project folders" as a problem. Like you said though, you would have to create over 100 queue topics, but is the issue just the time in doing that?