Those 3% is specifically the military part of expenses. The Scouts may or may not be part of that, but they're not going to affect the final figure much, since their fleet are mostly small ships, even if they do have a leavening of cruisers. The civilian side of the Imperial bureaucracy is not part of the military expenditures.I haven't read Grand Fleet either, but I use 1% for the Imperium budget (30% of world military spend from Striker). Also I assume a huge chunk of that 1% goes to support the Imperial bureaucracy, MoJ, Scouts and army, besides the Imperial Navy.
Hans