Sure, Presence will work -- but you have to cast it first. It may be PP-free, but it is still and spell and you need to cast it. I doubt dragons have nothing better to do with their time than keep casting Presence on the off-chance that some invisible, scentless, silent intruder has arrived in the last few minutes -- or concentrating on that one spell all day to keep it from expiring. For that matter, the Presence sense can be fooled, too. And with a range of 10', it will alert the dragon rather late in the intrusion. A surprise attack would still be rather effective and a thief isn't about to come that close to the dragon while trying to pick up some of the treasure off the fringes of the hoard. Any respectable dragon's treasure (i.e. like that in illustrations) sprawls well beyond the wyrm's body.
If the dragon is worried about some undetectable being penetrating his lair, he's better off making it difficult to access and employing some security measures such as subordinate monsters and traps.
Anyone who is willing to try assassinating a dragon should not be denied some small chance, given that failure will mean destruction and leaving behind a reputation for being a mad idiot, regardless of any former deeds.