IJ may not have a limit. The 1000 tags limit was imposed artificially on LJ in response to, as I understand it, server load - there's nothing inherent in the code that requires it, as demonstrated by the fact that we used to have so very, very many more than 1000. IJ has a fraction of the load of LJ and may not have ever implemented a limiting feature. There's nothing I can find in their documentation or FAQ that indicates if they do one way or the other - probably that's the question to get answered first before we try to hash out any kind of system.
That said, one thing easy enough to deal with now: I feel like the "in-joke: " lead on the in-jokes kind of... kills the joke. Odd to say, but we could actually learn from F_W in this (their fandom tags are all "fandom: twilight" or whatever, but more freewheeling things like "think of the children" just... are).