If you still need to solve your problem then message me, I know exactly what you're trying to achieve as I have just spent the last four hours making this happen on my own site.
I have hidden subcategories but I know exactly how to make the products within these categories as active as can be.
It's quite easy but you should be looking at storing the products in a linked category.
Example...
- make a category called lingerie
- make a sub category called 34F (nice category :-)
- create a "mock" product in the 34F category and then disable this product. You only need this so you can cross link products into this category.
- disable the 34F category (now it wont show in the categories list)
- create your live products in the lingerie category.
- link your live products to the 34F category using cross linking copy method.
- now, simply mark your products as active in both categories.
Works a treat for me. If you need more help then just msg me.