Perseus has just about doubled my resource count (if I don't have them all yet, it may still reach that). The situation is almost beyond hope in the mobile space right now, but even on the desktop, this many resources is painful. Everything is slower and much more difficult to manage. And I expect (hope) that Logos will be releasing more collections like Perseus as time goes on (though perhaps not free).
I don't know if this would work for everyone, but I think it would be very helpful to have multiple libraries. Hiding resources isn't an answer - too painful and not dynamic enough. Well-defined collections isn't, either, since all the library, searching, and indexing overhead of the full-sized library is still an issue. But if I could switch libraries and manage which resources are in which, that would be excellent. I know I couldn't search across, for example, both all my N.T. Greek stuff and Perseus (if they were in separate libraries). But that might be a price I'm willing to pay for a better experience in my normal usage. Or perhaps one library was small and focused on normal usage and the other included everything (assuming a resource could be in multiple libraries). This could also be leveraged to make the mobile experience better.
Anyway, that's one idea on how to improve the everyday experience in Logos when one has a very large set of resources.
Thanks,
Donnie