I just released an iPhone app today. I have also implemented Apple’s Smart Banners on my website.
If the app is ONLY an iPhone app (although it will run at 2x on an iPad, but is NOT a Universal app), should the Smart Banner be showing when the webpage is viewed on an iPad?
According to the docs (link above) the Smart Banner will determine if it should be displayed on the device.

Question: Should the banner be displaying for an iPhone app only when viewing the webpage on an iPad?
I don’t exactly get your question. If you mean ‘will the Banner show up on an iPad?’, then the answer is yes, the Banner for an iPhone-only (not Universal) app shows up on an iPad (if you meant ‘should Apple change this behaviour?’, then this is a subjective question).