Like everything else, it depends.
I found the agitation method to be cheaper and more flexible. The pumps are inexpensive (approx. same cost as aquarium pumps), and the tubing at $3.50/25' is cheap too. The reason I didn't use the aeration method was because the aquarium pumps did not provide enough volume of air to properly move the water around, nor did I have a compressor. I also found that the airstones used by Fibergeek (approx. $3/ea), and the quantity needed to provide adequate coverage makes aeration much more expensive. In my case, the agitation method also took up less space in the bucket than did the aeration method. Weighing down the airstones to eliminate the bouyancy was also a pain to deal with.
It's a matter of economics and scale, each situation will be different. For the small scale home/hobby anodizer the agitation method is easier to setup, cheaper and has the added bonus of reducing misting and you can watch the process if you are so inclined. Not that there is much to watch, but with the aeration method, you can't see your work piece due to the bubbles.
Multiple tanks or large tanks can be accommodated by either using higher capacity pumps or multiple small pumps and it may be more cost effective to use aeration for these type applications. But, in these cases, rather than using any pump and tubing at all, I would probably use a mechanical agitator. Since the purpose of both aeration and agitation is just moving the water around, even a paddle wheel attached to the end of a small motor or a variable speed electric drill would provide the movement required.
Multiple tanks would require multiple pumps unless you have a central reservoir of electrolyte, along with a method to drain off excess solution from your anodizing tanks to feed the pump. This isn't something I was attempting to address with this method, but was more geared to the hobbyist/small scale anodizer.
For me, using the LCD Kit sold by Caswell with the 5-6 gallon bucket for anodizing, the agitation method is just plain cheaper, easier to set up and safer to operate.
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