I felt compelled to login when I read this post and put my thoughts into writing:
I like this plugin. I appreciate the plugin author (Mike Jolley) for his hard work and time and dedication in creating something like this available for everyone to use, so thank you!
Just to be clear I am not a coder and therefore from my perspective I cannot possibly analyse the efficiency of the code that powers this clearly very powerful plugin.
It is great that Tabish has taken the time to detail his/her findings and hopefully help to improve the plugin in the long run, especially when he/she is clearly talking about hundreds of categories (I have personally never found the need to use more than 5 if at all) but just reading the title of the post, I can't help but feel that it is not the most appropriate description of the issue that has been identified!
Most users probably don't extend the plugin as much as Tabish has done, so would never encounter this 'too many queries' issue. I'm sure a plugin author is almost always pleased that someone is pushing the boundaries, but
"Think twice before using this plugin (WARNING)!!!"
sounds more like scaremongering, akin to tabloid headlines, and it might be LESS confusing and LESS misleading
to say specifically - in the title - something like
'Too many SQL queries occur when setting up hundreds of categories'.
Apologies if this is not the most appropriate title, and I hope I am being clear about what I am trying to say here. Ultimately, like vektor has said, I would love it if a solution could be worked out between both Mike Jolley and Tabish as I believe both will/have benefit, and non-power users (aka myself) will - unknowingly - also benefit, with thanks to developers like them, from a great plugin.