SLH 1ST GROW

Both plants have grown lots more foliage this week and little sister is now 40cm tall.. So much so that I've been quite drastic and done some defoliation at the lower levels on both plants. Also done some training to try and control cola directions of growth. I've changed the nutrient solution for more or less a 50/50 mix of veg/flower nutes. Was quite suprised when i lifted the top tier off my recirculating system to find a collection of roots about 60 cm long have passed through the clay pebble layer (10 litres of the stuff) and are permanently emersed in the nute solution in the reservoir. What's the point in me setting a watering schedule if its got roots in the reservoir? Should i be trimming these roots off or should i just leave them alone? Also, I've heard that super lemon haze doesn't like too much water, so surely roots in the reservoir can't be good? Anyway, despite my confusion and not really knowing what I'm doing, both plants appear healthy. They both have nice shiny leaves with healthy tips etc. Am I worrying unnecessarily? They do say 'if it ain't broke, don't fix it'. Any suggestions would be greatly appreciated. Also I'm not 100% on this, but i think this might be the start of the flowering stage which is why I've changed my diary entries to flowering. I'm sure i can see a few little white pistils here and there, but they are tiny at the moment and my eyes are crap.