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First, all senses except for olfaction are routed through the thalamus, not the hypothalamus as you say. That said, olfactory pathways do go through the limbic structures associated with emotion and memory (the amygdala and hippocampus, respectively). Many researchers believe that this anatomical pathway right into our brains' emotional and mnemonic processors makes the cognitive and affective influence of the sense of smell far more insidious as we are less aware of such influence than we are aware of the influence of information associated with our other senses.
So what does this mean? The larger social question seems to be: Are we okay with advertisers taking advantage of our human, animal natures? Appealing to our emotional responses bypasses our rational, cognitive capacities (which for some people seem to be highly questionable in the first place). Scent advertising is but the newest version of this, and I'm sure that Karl Rove is already looking for ways to leverage this phenomenon. What's truly insidious is the formation of new associations in our minds between pleasant-smelling, emotionally appealing fragrances and some product or idea somebody is trying to peddle.
Aren't these cognitive abilities among the very foremost traits that make us human? While some advertisers appeal to our pseudo-rational abilities (e.g., 'Buy Super-GLO - it does everything that 5 different cleaners do!') many others appeal to our emotions (I'll admit that I've gotten dewy eyed at more than one Kodak commercial). Using scents to appeal to our emotional selves is but one more way to get us to "buy shit we don't need" to quote Chuck Palahniuk's great line in Fight Club.
We are subjected to enough sensory stimulation overload on a daily basis, including our sense of smell. With pollution, car exhaust, cigarette smoke, strangers’ cologne and perfume – do we really need advertisers inundating us with smells?