This topic gets kicked around from time to time.
From what I understand, some experiments have been done where seahorses were inbred for up to 7 generations without seeing issues. I don't know if this is correct or if it will hold true for all species because we try to avoid inbreeding as much as possible.
Every breeder as a different approach. When possible, we started with WC specimens. On occasion we have added WC into the mix but this is the exception rather than the rule. Managed correctly and barring disasters, it isn't necessary. This is especially true if you have multiple pairs of brood stock and put new pairs together from different lines.
A good breeder will also cull defects and mutations. It has become popular to sell these for a lot more money but we still resist and pull them. We try to remain somewhat of a purist and keep the lines clean. My fear in selling them is that folks will in turn breed them and then there will be a lot of mutated seahorses around. As a rule, I don't believe them to be as hardy.
Purchasing from different sources doesn't always guarantee different blood lines. Many breeders buy brood stock from other successful breeders, this happens at both the hobbyist and commercial levels. Even when buying from resellers, the seahorses may have been overstock that was sold off in large quantities to wholesalers and retailers or to wholesalers who then sold to retailers.
To say CB haven't been exposed to pathogens is a misnomer. CB seahorses can potentially be exposed to higher levels of pathogens than WC, however the range of pathogens they are exposed to is smaller. Any closed recirculating system can quickly have a build up of bacteria, fungi, viruses or ciliates. Many of these are ubiquitous and are ever present in small numbers. With high densities and/or poor husbandry, they can take off or take over. What they are not exposed to are parasites that require multiple hosts to complete their life cycle. Anyone who has tried to raise fry and lost them has seen a build up of bacteria or ciliates.
I don't believe in the idea of exposing a seahorse to pathogens in order to build up immunity. Immune systems are innate. If one was to expose them to say a certain species of bacteria, it may not infect the seahorse right away and be waiting for an opportunity to take off. Then when the seahorse becomes stressed from a stressful event or exposed to persistent low level stressors, the seahorse becomes sick and dies.
CB seahorses are easier than their WC counterparts in aquaria. Besides the obvious of already being trained to frozen foods, they are conditioned for the environment as that is all they have ever seen. They are used to higher densities. Sometimes WC never adapt, can sometimes be very difficult to convert to frozen foods, should go through a longer quarantine, be dewormed and may or may not breed in captivity. From experience, we found that when we purchased adult WC specimens the survival rate was very poor and few made good breeders. I suspect how they are collected, handling, feeding and stress play a major role in this. All specimens we collected ourselves did very well.
Dan