* How can we be scientific about ATS and provide empirical data to draw the correct conclusions?
I cant say the scientific things about ATS but Im using it and the result is awesome
getting the scientific data that you refer to would require some pretty expensive equipment. Getting relevant data would require that the person running the experiment actually understands how to properly construct and maintain a scrubber, and has access to pretty expensive equipment. For now, all we have is the proof of thousands of people worldwide successfully running scrubbers. And it is thousands.
* For what kind of tanks can an ATS be beneficial or dangerous?
I dont think that ATS could be a danger for any kind of tank. I saw it on fish only tank and I have it on my reef tank. as long as those algaes are in a safe zone there would be no problem, even when they are in tank they will be eaten by Tangs really fast!
Scrubbers have an extremely low chance of being dangerous to a system if constructed and maintained properly. If Alk/Cal/Mag dosing is done with 2-part type supplements and no water changes are performed, then the ionic balance can get skewed due to dilution, and an occasional PWC should be performed. If a calcium reactor or kalkwasser is used, this is not an issue, but the occasional PWC can't hurt, and by occasional I mean 5-10% every month or two. Again, not easy to test ionic balance, so I err on the side of caution.
* Light sources - can LED be more than experimental for ATS?
yellow leds are good,remember that ATS need a light with low kelvin.I use FPL Fluorescent with 2300K.
No, yellow LEDs are not what you want. You want 630nm and/or 660nm red. No whites of any kind, there's not enough red or blue component to them to do anything. If anything else, throw in one 425nm blue (looks violet almost) or 455nm blue (royal blue) for every 7 or 8 reds.
* Skimmers in cooperation with scrubbers - Advantages and disadvantages.
i dont think that skimmer is necessary for soft coral reef tanks( for SPS i think it must be) cause its eliminate the foods that Dissolved in water.believe it or not its been 6 month that i remove my skimmer cup and its only job is feeding air on water and every thing is really good condition with ATS.
All corals prefer to have massive amounts of food in the water column. Coral reefs have an incredible amount of food floating through the water column compared to our tanks. On person's tank (you know who), which is a 90 gallon system running 2 100-gallon rated scrubbers, has been running a continuous feeding system and recently achieved a food sautration level of approximately 50% of that of an actual reef and the dual-scrubbers could not keep up, and the corals were not adversely affected.
Excess food (organics) in the water do not adversely affect corals. Excess waste (inorganics) do. Skimmers remove organics before they can become inorganics. Scrubbers remove inorganics after they have been digested by the tank inhabitants. That is the (main) difference. If you run a tank with a skimmer only, then you will have low food and high waste (need PWCs). If you run a tank with a scrubber, you will have high food and low waste. If you run both, you will have low food and low waste.
* Scrubbers and carbon dosing - Competition or cooperation?
* Approaches to achieve 3D-scrubbing in both open and closed designs
* Ozone and UV combined with an ATS - good or bad?
i didnt have experience about that3 questions
Carbon dosing (I'm not an expert, so forgive me if I screw this up) is basically feeding the bacteria so the colony can grow faster and consume waste at a higher rate. It is effective at reducing waste, but this technique works in direct competition with the function of a scrubber, so they don't play well together - your scrubber will suffer because the bacteria 'get there' first.
You can get 3D in an open box if you put an enclosure around the screen with the bottom open (like if the screen terminates into a sump chamber). You will get some 3D growth. Closed bottom will probably get a little better. Either way the submerged section will get little if any growth.
Ozone and UV are not something I know a lot about.
* Effects on livestock - Good and bad
good. more pods and amphipods. and the algae that you'll collect will be a nice , fresh and really healthy food for all of your fishes specially tangs and clowns and damsels
+1 on pods. Microscopic food particles are also left in the water column for these guys to feed on in the tank so your pod, sponge, and filter feeder growth in the tank will explode.
* Long term usage of an ATS and how to collect data about it?
I use it for about year and the half and I haven't any problem for using it in my tank.
ask me and if I knew about it I'll share them with you 
Right now 3 years is about the longest that the vertical waterfall type scrubber has been around. I have been using one for just over a year and have had little if any problems, besides the situations I created myself.
* How to avoid crashes - what are the safeguards?
the only problem will be Water pump failure. Have a good water pomp have a good ATS!
+1, cleaning said pump more often will lengthen life as well.
I just read this the other day regarding metals in DSBs.
Coral Magazine, Nov/Dec 2001, page 89:
"The primary material that cause trouble are metals, especially the toxic heavy metals that are often called "trace elements". These toxic materials are often added by aquarists in excessive amounts as additives for no good reason, and in most cases they become poisons in concentrations above those in natural sea water. In addition, most organisms get all the "trace elements" they can use from well-formulated foods."
"In most cases, actually more of these materials probably enter the reef tanks in foods than in additives, and after they get excreted by animals and dissolve in the water they get bound directly into the algae that need them for growth. Fortunately, algae are often exported from reef tanks, keeping the level of trace metals low".
Many hold to the theory that "old tank syndrome" is caused by a buildup of heavy metals. Algae does absorb most heavy metals, however the rate of absorption is not well established. Better than NOT absorbing them at all, however.
