No, I think the sub-catagories serve a purpose in organizing categories and the MyConnections function is NOT a good enough reason to upend everything for a complete restructure, which would take months if not years to address all the categories and we already have quite a few that are put on hold for changes already.
It should be possible to code MyConnections to also search through sub-categories. It's just not implemented yet. It likely would only take a few lines of code and a couple weeks to do, depending on how easy it is to detect sub-categories in the API.
EDIT: As Chris pointed out, MyConnections also does not do multiple pages at the same time right now. It could if you sacrifice calculation time and add an updating loading bar indicating how many profiles are left to check.
However, adding a sub-category routine could mean a higher server load depending on the size of the category -- especially if say, someone ran it on the top-most census category and it attempted to propagate through the entire tree.