I haven't noticed any downsides of using Weed-EX, except if you try to right click with a 1000mB Universal Fluid Cell full of the stuff, and the plant is already maxed out, it will place the Weed-EX liquid into the world (destroying your crops).
But the same thing happens with water.
I've noticed all the guides seem to say avoid Weed-EX like the plague, but I've gone from vanilla seeds to avg. mid-20s with my cropsticks saturated in Weed-EX. I never have been able to sustain plants at max stats, though... still need to experiment...