Does black thumbs affect the food you get from industry from the sower affinity? And if it doesn't does anyone know if this works well?

Nope, the malus it's calculated before the affinity is applied. Can be very worth to take. However remember it will affect any food improvement u will build on systems ( i never build those anyway with sowers ). Spendthrifts trait can be also good ( industry to dust conversion works same way ) opening points for other traits : i usually take legendary heroes for the lv3 admin hero ( its a blast, industry and food at the same time ) and sometimes even nway fusion plants+core mining. Always switch metallic waters with mineral rich + 1 level of optmistic.