Yes, because I need a chest to take up 7 times as much space as it normally does. And this assumes that the top of hoppers are wide enough that you can't click between them and another block, something I haven't checked yet. Overall, hoppers are nice for automation, not security.
Well if your hopper is under the furnace and the furnace is a block above floor level your Hopper should be protected by the floor from there It can auto feed into the chest which could be in a blocked off room. You could probably auto feed the fuel too if you wanted the furnace itself underground. This probably sounds confusing so I can set up something in BB if you'd like
The point is that you still have to block in the chest, even if you leave space above it so the hopper can work. Putting it in another room is a tidy solution, I'll give you that, but you still have to block off that room. If you're going to block things anyway, why not just block the chest, and only put things in the furnace when you need them?
And as stated above, realistically why not just lock your house? I mean, I don't block my furnaces because nobody can get to them anyway, so i don't need to block chests, or try to use hoppers as a security measure, either.
And I did check out hoppers more today, they do take up the entire block space they're placed in. So you can't click things down their side or at angles, it just clicks the hopper.