You can do both. People like to use pots so they can move them around and rotate the plants and stuff. Also there are some pots that will air prune the roots. You can also fill your entire tray with grow rocks and put the rockwool cubes right in there.
If you experience algae you can cover the top and have them plants poke out of them. If you don't flood too high you shouldn't have to worry about that iv'e found out.
As far as numbers, check my journal out bro! I did 25 plants in a 4x4. I would do 20 if I were you though. Also, keep veg to a MINIMAL! Seriously man, mine exploded once I flowered them. As a result, my garden got too crowded and they were fighting for light and grew into each other. I vegged for 4 weeks so id recommend 2 MAX. Check it out in my sig.


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