I don't think trending hashtags are a good idea, but if they are being added then have the trends limited to the current instance only. I think gnusocial does it that way.

That is, avoid creating global signals about multiple instances. Global signals will be used to cause disruption. They facilitate celebrity cults or the dogpiling of particular users. On Twitter we can see how this kind of thing works out.

In technology as in biology, loosely coupled systems are what tends to work. Global information tends to result in monoculture and allows a problem in one place to rapidly spread everywhere.