The short answer is yes, the time of day you book kind of affect the prices. The longer answer is, but not really. In many cases, we have seen that travelers who search for flights on Tuesday around midnight save about 6% on their flights, making this the cheapest time of the week to book.
Contrary to popular belief, booking airline tickets late is most of the time cheaper. Airlines are well aware of the urgency of business travelers who mostly book their seats at the last minute and pay more for their flights. The logic hence says that the earlier you book, the less expensive your seat cost will be.