I.M.H.O. aka merely Opinion.
1st: Individual boxes, definitely. It seems, at least to me, that multiple nuc colonies in the same box with dividers just do not do as well. Could be a variety of reasons. One that I have no credible recorded data for but makes most sense is simply bee pheromones. When all in one box with dividers it is near impossible to not have their scents mix. What affects one colony tends to affect the rest. If one of the queens stinks or perfumes particularly well, she repels or draws more bees from close by; affecting the other colonies in the box. Having them in one box that matches the rest of our equipment is certainly convenient. However, if you put your true bee-man hat on and reconsider the great lengths we go through to keep colonies apart when doing hive manipulates dealing with problems; such as combining colonies, introducing a new queen, halting robbing, disease control, etc. ... the Bee Senses should be clearly telling us to keep them in separate boxes. Those separate boxes can be placed very close together, but each is best as a stand alone, not integral to the one next door. For convenience absolutely the dimensions of these separate boxes can be made so that when placed close against each other they fit onto or within our other equipment.
2nd: Number of frames. Depends on your intent.
- If just mating and harvesting queens for immediate use (eg new splits, sale, or donate), 2 frames of any size, including the minis. Soon as she's proven, cage, bank, and distribute.
- If keeping a queen in reserve to emergency re-queen, 3 frame of the standard you are using in your main colonies (eg: deep). Keep her primed and mildly active. Harvest brood weekly so she's active and always has some room. When needed, cage her and take the brood frame with her. Introduce to the new hive with candied cage hole, on HER frame of brood.
- If keeping a colony in reserve to replace a lagging failing hive or dead out, then it is a 5 frame of the standard you are using in your main colonies (eg: deep) or a full box with a follower board. Use the 5 frame to combine and take over a failing hive. Move the 5 into a standard box, take apart the failing hive leaving the bottom box on the bottom board. Shake all the old hive bees into that bottom box. Place newspaper on with a few slits in it. Put the new box (5fnuc) ontop. Put the rest of the hive back together. Use the nuc to re-populate a dead out.
Hope that helps!