Currently the crafting table and the advanced crafting table do not support NEI ? shift-click with recipes that use tools. Other mods like AE2 or Forestry don't have that problem and support that feature even with GT Tools.
It would be great to have a third tier crafting table, e.g Elite Crafting Table or Professional Crafting Table that allows for shift-clicking, ideally also using the items in all of it's storages (as well as the adjacent inventories like the compartment drawer etc).
Since being able to craft with NEI ? shift-click is much more comfortable not having the normal table and the advanced table supporting it is fine (balance).