Is there greater merit for one who memorizes the Holy Quran with the verse numbers in addition to one who memorizes it without them?

There is no legal text that proves that the one who memorizes the Quran by verse numbers has a greater reward. The advice is not to do that and not to care about it, because it is a door to showing off and a waste of time. What is more important is to focus on perfecting recitation and memorization, understanding the verses, pondering their meanings, and acting upon them. This is the ultimate goal of reading and memorizing the Quran. The Companions would not move past ten verses until they learned their meanings and acted upon them.