||A very interesting question! Unfortunately, I know of no research into this. This is certainly something that would be worth studying in a controlled setting. I suspect that the answer is yes.|
The chemistry of the human brain and other body systems varies throughout the day... for example, melatonin levels are higher at night. It seems very likely that varying levels of neurotransmitters, enzymes, etc would result in slight differences in how your body reacts to and metabolizes drugs. I suspect that the differences would not be very large though. Its also likely that different drugs will be affected by time of day differently, and that different people will have varying degrees of sensitivity to daytime-related drug effects.