I think I would personally regret it if I weren't able to look through the sides. You'd probably find yourself constantly having your hands in the trough to pick up frags to check the growth. I would keep the extra water volume of the 50 gallon just for stability, and then replumb the skimmer and have the 50 gallon AND the through for frags (double the volume!). Now you can be an official farmer
. But maybe try it with both just so it won't be that hard to revert back if you regret it.