Ok, here goes my 2 cents...
"When your using the grow beds you're removing a lot of soil biology that normally would interact with the plants. Does that have an effect on the benefits the plants offer im not sure."
In reality and IMO your not prohibiting this relationship, using creek gravel or clay it acts as a filter for the solids and bacteria will grow and break these solids down, after all it is organic matter. Plus adding compost worms to the system will really boost this eco system. As far as the health of the plant or the nutrition content of the plant that is decided by what you feed your fish, dirt farming is no different its what you feed the soil. Example would be this. The plant absorbs what is in its "soil", so you have an organic carrot that was fed compost, the compost came from a commercial non organic farm. That farms soil has been depleated and no longer contains the trace minerals, so the compost contains no trace elements so your carrot does not either. If you feed those tops to the tilapia your system will not contain the minerals either. Same goes with the crappy commercial fish food. But if you are feeding your fish wholsome nutrient DENSE food (from your garden), your system will contain the same thru the fish waste. Another Suggestion would be seaweed if your by a coast, this stuff is packed with trace minerals so I read. As far as getting protein there are several ways, make a 5gal bucket and put fish endtrails in it, drill holes near the bottom the let the maggots drop into tank. Vent out the roof of greenhouse, just got to get creative.
"You can grow more calories in a small space which could mean that you are having less impact."
This IS the case with aquaponics, in dirt you are limited by many factors and space is one. Space is a factor due to these factors, 1.) nutrients and 2.)water. There are only so much available nutrients and water supply per sq ft. In a aquaponics system you are really only restricted by actual space and light, your water and nutrient supply is never ending and thus elimitating the peaks and vallys associated with soil. This boosts growth and increases production ALOT.
"But most folks who are doing aquaponics use a commercial fish food which is a by product of the large commercial fish industry that are destroying fish populations. They also include different agriculture products that are grown far away then heavily processed then sent to you.
You can supplement your fish food with BSF or duckweed but they don't meet the full protein requirements for the fish to keep up good growth."
Again, the maggots are a good choice to suppliment as well as black fly. Duckweed is still pretty high in protein @45%
"Then there is the whole plastic problem. You may be growing in a smaller space but with all the plastic piping and tanks the chemical foot print your garden is using increasing dramatically. Most of the plastic is PVC which is a pretty nasty thing to make and has lots of toxic by products. Its made far away in villages that we dont have a relationship with so we can still feel like we are not making a big impact."
You can use poly tubing, copper or steel. I totally understand here and PVC is not the best choice at all, it off gasses some pretty bad stuff. I personally use poly tubing, over the life of this tubing in the system (forever) the benefits WAY out weigh the "cost". Permaculturally speaking this is a good thing.
Does anyone agree or disagree?
I hope this helps and provokes some thoughts