Okay so I don't have a dog of any breed that comes in merle (well okay Kim probably has some merle-potential breeds in her somewhere but as she is a mystery mutt and spayed at that, it really doesn't matter), so this is coming from my Flat-Coat perspective:
I think it's almost universally agreed here that breeding M/? X M/? in the more common breeds we see in the U.S. -- Shelties, Collies, Aussies, BCs, Great Danes, etc. -- is morally reprehensible due to the documented fact that double merle pups born in those breeds are clearly at high risk of suffering from serious defects and there are many, many m/m dogs (often even littermates or closely related dogs to a desired merle) to choose from for a given breeding.
Dachshunds are an interesting case to me in that they are a breed that also has very minimal white in general and which comes in merle...and sometime double merle. I don't know what if studies have been done on the rate of detrimental effects of M/M in that breed. But since some M/M's clearly do cause serious issues and the merle gene is not particularly common in Dachshunds, there's really no reason for an educated person to take that risk when choosing a potential breeding pair.
Catahoulas and Koolies are, to me, somewhat different in that right or wrong due to historical selection the majority, even the vast majority, of their population is currently merle. Which leaves even well-meaning and very educated current breeders with the choice of either breeding in solid dogs of other breeds, breeding merle X merle, or losing a large swatch of their genetic diversity.
There are a lot of claims made about the incidence of deformities in M/M dogs of these breeds. To my knowledge there is not currently a reliable test for the Merle gene (please correct me if I am mistaken) since earlier ones were proven to actually be indicators of piebald and not reliable when it comes to merle so even people testing and keeping track would be making educated guesses. The relation to white markings makes logical sense to me but whether that's really true or how that relationship works exactly...I don't know.
What I do know is that the loss of genetic diversity in a breed is devastating. Look around at the purebred world and this is more than evident. I would hate to see the Koolie breed go down that path. Who knows what else is lurking in those genes that could crop up with increased homogeneity? Merle is, as others said, relatively easily identified...not all conditions are, and some can be downright infuriating to identify and trace.
So while I'm not and never will be a promoter of M/? X M/? breedings and the 1/4 chance for each individual to be M/M, I would much rather the goal of becoming a m/m- and M/m-only breed be a gradual and intelligent process and could not in good conscience universally condemn folks doing merle-to-merle breedings along the way. And with education, any luck, and a bit of faith in humanity as a whole I like to think that acceptance and use of solid dogs will become more and more popular...from what I'm hearing it's already trending that way.
/novel