I know naming conventions for tables used by plugins generally start with the name of the plugin and then the model pluralized. For example lets say I had a plugin called Poll, with a model also called PollPoll and another model called PollTag then the resulting table names would be poll_polls and poll_tags. They would also have a habtm relationship so what is the convention for that table name? I believe it would poll_poll_polls_poll_tags, although it is a little redundant it makes sense since the first poll_ represents the name of the plugin, while poll_polls and poll_tags relates to the models.
Also have any naming conventions changed for plugins in 1.3? Is the above stated correct?
Not sure about cake 1.3 (I'm not using it yet), but this if you're right this sounds like a perfectly acceptable case of breaking convention and defining the jointable, and foreign keys in the model relationships and possibly in the plugin.
Why does your plugin require a join table? Seems like a design issue. Perhaps there is a case where this is needed, but if I had a HABTM relation with a plugin, I would add a modelname column to the plugin's table, rather than have to create a new table for each model I wanted to use the plugin.