Hey bud,never be sorry for asking questions,helping new growers solve problems is the reason i use this forum ,there are other hydro growers who feel the same too.
Anyhow yes,your on the right track ,the plan you posted sounds very much like how i grow,i will explain my grow better if you need but lets address your questions 1st.
You asked about humidity issues with a table full of medium like hydroton,think of it like this,every time you flood the medium gets soaked,this is what keeps the roots & plant alive,but after the flood the surface area of the medium starts evaporating & eventualy the interior of the medium as well,this moisture is 1st released up into the dense growth of the canopy which increases the chance for powdery mildew all over the entire plant as well as the dreaded grey mold inside the budd,if you get either powdery mildew or bud rott bad enough the whole grow is in jeapordy ,using a cover on the table instead of a medium eleminates any chance of increasing the risk of either issue.
Then the moisture goes into the ambient room air incteasing overall humidity,if your lucky enough to have naturally low rh then its best to keep it low,a level of 20% in bud is better than having a rh thats 60% in bud.
In hydroponics roots are king,plants feed from the root tip,the more root tips & fine hairs comming off the roots the more the plant increases its ability to feed,we want as many roots as possible,roots need dark to grow & any light stops growth cold.
I use 5 inch round net pots but any net pot would work,i like the 5's beacuse they are easy to handle & for my method the small pot size allows me to improvise further,you can use square or round but i wouldnt go any smaller than a 5 inch,this way the heart of the root mass has something fairly large to adhere to creating more stability.
When you fill the net pot with medium & put the plant in the medium roots will start growing into the medium,this locks the plant in place,if the outside of the pot is not blocked from light the roots that are growing within the net pot will automatically prune the growth,stopping any roots from stretching outside the net pot,pruned roots limit the plants ability to feed,as soon as one little root tip hits the light its pruned,you want to avoid this if possible.
You asked about the rockwool cubes,imo you should get away from using any rockwool at all,its an outdated material that suffers several drawbacks like ph & over watering issues,cube compression is another drawback,i stopped using rockwool in favor of sponge plugs,i use root riot brand & they work just as well as rockwool, without any of the negative issues that go with rockwool.
When you transplant you shouldnt use huge cubes,you want as much stability as possible,the larger the cube or sponge the less stability,i get the most stability using the 1 inch plugs,letting the roots stretch out an inch or so before putting them in the net pot,then i make sure to keep the top of the cube very near the top of the pot,when you bury the cube too deep the chance of stem rott increases.
Just remember that root mass means bud mass,do everything you can to block light from hitting roots at all phases of the grow,especially in veg stage because veg stage is when most of the rapid root growth takes place,if i were you i would use flood & drain for veg as well as bud & cover both tables,this way when you put the freshly vegged plants into your bud table your plants will allready have a root mass that extends 12 to 18 inches out of the net pot,root growth slows greatly durring flowering phase.
The rockwool cubes just sitting in the table with no medium will not be harmed at all from roots growing out the bottom of the cube,if it were my grow i would only jump up one block size or no additional blocks at all,a 1 inch block is fine as long as its going into a medium filled net pot when the roots are an inch long, then cover the table before roots overgrow the new cube,roots will be light pruned in the cubes the same as net pots as soon as they see the light & air.
You dont have to transplant either,cover the table,cut snug holes,transplant the 1 inch cubes when roots stick out an inch or longer directly into a 5 inch net pot filled with hydroton,keep rockwool cube near the top of the pot,about an inch down from the top,then insert the net pots in the pre cut holes in the cover,set timer to flood once every hour for 15 minutes,leave flood times at that setting until your in heavy bud,in heavy bud increase flood times to twice an hour with 15 minute flood times durring lights on leaving flood times at one 15 minute flood durring lights out.
The idea of covering the table is not new,most manufacturers sell hard plastic lids for the exact same purpose,when you enclose the table it brings flood & drain more in line with the aeroponic method,the enclosed enviroment retains a fog of nutrient laden moisture accessable to the root tips to feed from,i will never go back to open top flood tables this has worked so well for me.
If you need help installing the plastic i can talk ya through it,installing it isnt that hard its attaching it securely around the sides thats important,i can set a glass of pop on mine without any sag its secured so well using the clips.
This method also takes another issue out of play which is flood times,set it up & its a go.