Had the same situation a while ago. All lined up and ready to go, but no take-off clearance and no word from the controller. Turned out to be a scramble from the police helicopter, who was on another frequency and needed to cross my departure path.
Yes, it does make you feel vulnerable, even though there's no other traffic on the frequency, let alone traffic receiving a "cleared to land". A "line up and wait, expect departure (take-off?) clearance in xx seconds/minutes due to ..." would definitely give me more sense of security, that the controller knows what he's doing.
Plus, aren't conditional clearances like this only given above certain weather minima? Such that a landing aircraft (or an aircraft taking off from the end, while you are lined up and waiting at an intersection) could see the whole runway and thus spot you before it's too late?