I'd like to have some kind of folders, to divide triggers, scripts and macros by category.
Would also be nice to be able to enable/disable all of the above by category.

And just to be greedy, add subcategories too :)

For categorization you can create files in the batclient/scripts directory and keep your triggers split out by category. For example I have a tzarakk.bcs file with my tzarakk specific triggers in it. I've seen examples where you can turn on/off triggers by setting a client variable, but there is no ready made solution for this that I know of.