In the male quarters, how exactly does the male crew of the Thousand Sunny sleep?
TL;DR: If a 7th bed was needed Franky would have build one, but it doesn't seem like any of them should sleep on the floor against their will even if they only had 6.
To begin with, the pictures you showed were after Franky had joined. So whether he built a pirate ship for 5 male crew members and added a bed for himself after he joined or he put it there from the beginning considering a new crew member might join, Franky would easily be able to just build a 7th bed if needed. Heck, he could build a pretty sturdy bridge just on the spot in Thriller Bark.
Additionally, Oda confirmed that there should always be two crew members awake at all time. In the SBS of Volume 74, Chapter 737, Oda mentioned the Strawhats' daily schedule. He also said that at all times there should be two crew members awake. One should guard the front of the ship and another should guard the back of the ship.

D: I would like to know the Straw Hats' bed times and wake up times! - Penname fujiyama
O: I see. A very interesting question indeed. These people don't really follow much of a schedule but. In general.
And thus, even during instances where they have to navigate through the seas during nighttime, there will always need to be at least two people awake at all times in order to keep an eye out in both the front and back directions of the ship, hence every member alternates every 2 hours to stay on the lookout. It isn't too uncommon that these people don't get sufficient sleep.



On top of that, from chapter 699 it looks like they have enough beds as it is. Chapter 699 is the only chapter I could find where you could actually see the Stawhats asleep. At that time Sanji and Kinemon couldn't sleep jealous of Momonosuke and Usopp and Chopper couldn't sleep afraid of Doflamingo. Despite the fact that most of them were empty, you can see Luffy and Brook share a bed. Finally you can see Law and Caesar sleep outside. We can also see Franky sleepy, but outside guarding the ship as Oda mentioned. So whether Brook and Luffy always share a bed or it was just a coincidence, it looks like due to their random way of sleeping and with beds and couches all over the place, they don't even need al 6 beds to begin with.
Finally seeing Zoro sleep in a bed, it is safe to assume like you said that they all sleep in their beds as much as possible. Sanji does not sleep in the kitchen, Zoro does not sleep in the crow's nest, Chopper does not sleep in the infirmary bed, which is supposed to remain clean and sterile, and Brook does indeed sleep. Despite them sleeping in their beds mostly, they still don't need all 6 as mentioned earlier where Luffy sleeps in random places most likely and two need to be awake to guard the ship anyway.