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hydroponic Hydroponics - Thinning Mature Jalapeños?

Hey guys,
 
New to gardening here. I recently became interested in hydroponics and decided to experiment with an indoor DWC setup.
 
I started growing jalapeño peppers from seeds this past October. Three seeds sprouted inside one rockwool cube and I decided to just let them grow. While two of the plants started to outgrow the third, I thinned out the stunted seedling. I let the other two plants keep growing and continued to feed them House and Garden A & B nutrients.
 
Fast forward today, both plants look green and healthy. One is about 12 inches in height while the other is about 10 inches. The 12 incher started to flower about a week or so ago and it's now developing fruit after hand pollination. The 10 incher developed one flower but no progress was noted after pollinating and has considerably less buds. I'm using a 4' X 2', 8-tube Hydrofarm Agrobrite HO fluorescent light, 54W per bulb, running 12 hour cycle.
 
It seems like the 12 inch plant is dominant, as it's taller, thicker and has more buds. Obviously the goal here is to be able to harvest big, healthy fruit in the end. I know thinning is the rule of thumb in soil environment, however, I haven't been able to find a definitive answer when it comes to hydroponics. But the answer is becoming more apparent as the plants continue to grow.
 
Q1 - Is it too late to thin out the weaker plant?
 
Q2 - How will the root system of the dead plant affect the remaining plant, since I will not be able to remove it?
 
It is hard to distinguish which is which in the pictures but the one on the left is the 12 incher.
 
Any input is highly appreciated, thank you!
 

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