[__MatrixMan__]

The node operator subscribes their node to topics, so yeah that part is manual, and that's how the humans express their interest. You might have to update it every now and then if one topic is killing your battery or your hard drive or you just don't care anymore. The data which that topic governs is handled by the synchronization function which runs periodically without supervision.

Whether some or all of the data is encrypted is an application level detail. At the network layer you just call the function provided by the app/topic and it tells you whether to accept or ignore a datum, and which datum to delete if the storage quota for that topic is full. Lots of things don't need encryption (e.g. map tiles). Or if there's some kind of trust structure in place, the node may have keys necessary for doing the decryption--it's not like you're carrying data for apps besides those you're participating in.

As for the peer filtering thing, peer-discovery and synchronization would happen in time slots. So if it happens for 30 seconds each time and this app in particular gets 30% of that, then I guess you spend 10 seconds trying to see if any of those 10^12 peers are worth synchronizing with. Maybe you're checking to see if they're n hops away on your web of trust for that topic or something like that, it would depend on the case. But I don't see how this case has anything to do with mesh networking: all forms of communication are susceptible to DOS of some kind or another. The best we can do is limit the blast radius and maybe raise it to the user so they can handle the adversary out of band.