Stealth Cab Pots

Does it make a difference to plants weahter their roots grow verticaly or horizontaly?
I dont have much room available verticaly and 6-12 tall inch pot would take up alot of room, but i could get/construct a 3 inch by like 12 inch wide pot so i want to know would it make a big difference?
 
A quarter down from the top is fine. I also submerge water them. I like to water like that because it saturates all of the soil and it also replaces all of the gases at the same time. Fyi I can get away with watering every other day with this method.
 
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