Hopefully he will continue to do fine. Quite often, Pouch Emphysema (PE) is a single occurrence. In these cases it is no big deal.
I do have to applaud you for having a light stocking density. It creates a more natural look and environment for the seahorses. Usually ends up a healthy tank and seahorse life expectancy goes up.
When I refer to the organic load, I am referring to both dissolved and non dissolved organics within the tank. Dissolved organics will normally be in the water column and the skimmer can pull a lot them out. Non dissolved may be both in the water column and trapped in different places. Normal tests that we do on our tanks won't necessarily indicate that you have excesses in the tank. Theoretically, you can have 0 ammonia, nitrites and nitrates if the microbial population is high enough.
The problem with organic loading is something has to eat the organics in order for it to go through nitrification and de-nitrification. In systems with a high organic load there is normally a higher population of bacterial and protozoa. Doesn't have to be the pathogenic type or have the pathogenic gene turned on. Bacteria and protozoan are opportunistic and it doesn't take much for the flora to change to pathogenic types.
When I trouble shoot a system for organic loading, I look at the whole system, size, flow, filtration scheme, protein skimmer, substrate and rock, amount of feed and what is being fed, tank mates and cleanup crew etc. Sometimes it is obvious and other times it takes some digging to uncover the source.
A lot of old info recommends low flow for seahorse tanks. We find, higher flow, roughly a minimum of 10 turns per hour or more results in a much healthier tank. The seahorses become stronger, are typically more active and the flow helps wash everything through the filtration.
Substrate can sometimes be an issue especially with course substrates such as crushed coral. These allow a build up of detritus. Becomes a problem quicker in low flow tanks.
Sounds like you made a good choice with the protein skimmer. I am guessing you probably have it in a sump. Keep in mind, the protein skimmers efficiency or ability to pull stuff will be related to the turn over rate in the tank, how clean you keep the riser tube (depending upon design, skimmers can lose anywhere from 20 to 50% efficiency when the riser tube gets dirty) and of course how you have it tuned.
Filtration pads and sponges can hold a lot of gunk if they are allowed to sit to long without cleaning or changing.
I have also seen live rock really gunked up. This is usually a result of either too low flow or poor circulation through it. The worst areas are usually out of sight or in the middle of a dense pile.
Given the stocking density, I really would not expect a problem with organic loading especially in the first couple of years. If this turns out to be a single instance, I probably wouldn't mess with much unless you see something obvious. If it becomes a repetitive issue, then I would look long and hard at the system.