I have had both a/c and water-cooled engines in different replicas. Each has its own positives and negatives.
A/c pros: cost and availability. You can readily buy different levels of HP from local builders, whose main source of income is derived from VW Type 1 engines. Displacement and corresponding HP start as low as 1600 cc and 40 HP, up to 2332 cc and 180 HP or so. There are still a few quality engine builders available, with Pat Downs being one of the reliable stalwarts of the industry, and an active member of this forum. Of course, as HP increases, so do costs. Most, but not all, of our replica owners live within driving distance of a repair shop that still offers service on Type 1 a/c engines.
A/c negatives: Despite the current availability of a/c shops and mechanics, the trend is that the number shops and mechanics offering a/c engines is decreasing, as water-cooled versions of VW and Porsche engines, as well as water-cooled Subis, become popular, and the older shop owners and mechanics retire.
As the market segment contracts, parts become more difficult to obtain, with cheap Chinese imports for a/c VW's becoming the bane of reputable engine builders and replica owners. An additional concern for some is the lack of air con and reliable heat for the cabin, which can shorten the driving season.
Water-cooled pros: Modern engineering and design enable a 2.5 L platform to develop huge HP, if that's what the owner wants, as well as supply real hot water cooling and compressor-driven air con. Availability of parts and tuners is practically unlimited, with younger owners driving a vibrant after-market industry with an adequate supply of trained mechanics/technicians. Parts are readily available at reasonable cost. If you keep HP limits reasonable, i.e., at 200 HP or lower, reliability is almost assured.
Water-cooled cons: While Japanese second-hand engines are mentioned as economic alternatives, many buyers are uncomfortable with "running take-outs", and will only consider rebuilt or new engines. Cost can quickly escalate if high HP becomes important. Effective cooling can be costly, especially as HP increases. Proper cooling system design is critical, and our replica platforms don't offer the ideal environment for radiator location. In addition, expect at least a slight weight gain with a Subaru engine.
On a personal note, I have encountered and overcome almost every problem imaginable with a 350 HP Subi turbo engine in our replicas. Those problems were difficult and expensive to rectify. Overheating was the most persistent problem I had to resolve. Be aware that our cars are neither fish nor fowl. There are a number of automotive-related shops and businesses that will not touch our cars, even with a/c VW engines. A number of reasons are given for refusal: insurance, unfamiliarity, etc. This refusal ratio increases with a Subi or other water-cooled engine.
If you're not a wrencher, and you have a favorite shop that you currently use, go have a chat with the owner. Tell him your thoughts and options, and find out if he and his guys will continue to provide service, and if that service is predicated on an a/c or water-cooled engine. If he opts out, find out if he can recommend someone in your area, and then go talk to him.
There is no single platform, engine, or tranny that does it best for all of our needs. Determine what's important to you by ranking reliability, cost, service, longevity, miles/year, and all the other facets of replica ownership. What makes sense for me, at my age, may not make sense for someone else.
The supply of parts and technicians/mechanics for our replicas is driven by demand. Air-cooled engines still have enthusiastic hobbyists, but the trend is toward water-cooled. Nothing wrong with bucking the trend, as many of us have done for much of our lives, but the reality, IMHO, is that the air-cooled market segment will continue to contract, making reliable parts and service more problematic in the future.
Best of luck in whatever you decide!