Someone has mentioned Xero here in the past and I use it myself, but not integrated with the store in any way.
The general idea is to use the reports tab in the store to create an output that suits Xero.
Regarding the categories.. yes you can have any number of subcategories, but think very carefully about how you are going to organise things in advance. There are features to cascade products upwards through parent categories or not, and products can be in multiple categories as well... all of which can greatly affect the usability of the catalogue for buyers.
Regards
Rob