Tor hidden services are not nearly as weak to this attack, because they are not usually run as relay. Tor hidden services are weak for their own reasons though, mostly because it is very easy to find their entry guards. And after you find their entry guards you are only one hop away from the hidden service. A hidden service on Tor opens a new circuit for every rendezvous point a client asks it to connect to. So if a client adds some bad nodes to the network, they can then force the hidden service to open like two thousand circuits and send it a stream modulated in a certain pattern. Then looking for this pattern in their flooded nodes, will quickly identify three entry guards the hidden service always enters through. Now they are one hop from the hidden service, and have various ways they can attempt to compromise the entry guards or hidden service from this positioning.
I would suggest Freenet in darknet mode for a content store. But even Freenet is not that hot, the biggest issue being that content is not encrypted in layers but rather a message is encrypted one single time and then travels through series of encrypted tunnels. This is bad if the encrypted data is known by many people, but if you are storing unique content that only you access it is not as much of a risk.
The solution is to have i2p eepsite gateways.
Having a server that runs i2p, and then forwards traffic for several eepsites over a vpn. When the eepsites themselves go down, no big deal.
Having more than one gateway for all those eepsites (more than one machine with the same private keys) would provide redundancy.
Start doing this on a large scale, lots of...eepsite clusters behind a gateway and you've a weener.