Hi chrisisinclair,
Welcome to our Mattress Forum! 
Generally, it’s best to follow the mattress manufacturer’s care. this said I oftentimes find in my research many conflicting opinions about just about every issue that concerns mattresses. Some of them are coming from people in the Mattress Industry that have decades of experience and I respect and consult often. Trying to resolve conflicting information from different sources can become a vast and difficult task. The best approach I found is a “blend” of science and intuition as usually both left and right-brained thinking by themselves can end up being misleading.
It is generally accepted that Latex breathes more than other foams and that natural latex also has an inherent resistance to mold and mildew and would have less likelihood of developing mold and mildew for these reasons. It’s also true though that the development of mold and mildew would depend on a combination of several factors coming together. One of the most important of these is moisture (from the environment or the person on the mattress), one is the types of mold or mildew spores that are in the environment, and one is a food source (cellulose is one of these). For example, the temperature difference between a mattress and a solid surface foundation can play a role in condensation which would increase the odds that mold or mildew could develop. A cover or better yet an insulated cover on a foundation could help with this temperature differential vs just having a mattress on wood or metal.
How much of its beneficial qualities of cover and latex layer under the protector are “canceled out” depends on the type and fiber that is being used in the ticking or mattress protector.
A mattress breaths from all sides and you may want to consider a PU protector with breathable sidewalls or pads that have no walls at all, or as you mention … there is nothing wrong with cutting the side panels and sowing some sort of elastic band if you find just the right protector.
[QUOTE] 1. Has anyone used any of the membrane type protectors for extended periods of time (years) on a latex foam mattress and can comment on the condition of the foam? Did any of it mold or did any of it (especially the top layer of foam) start to turn a darker color or harden or flake? [/QUOTE] ….
I used a protector for more than a decade for my child’s all-latex mattress and I did not observe any development of mold/mildew. The latex layers were still in great condition even though I live in a humid area. (uppermost layer was 30/70 blended Talalay)
There are thousands of protectors with various cubic feet per minute (CFM) to assess the air permeability and also various Moisture Vapor Transfer Rates per day (MVTRs per 24 hours)
This is itself would great search criteria for protectors, product and material comparisons if anyone has time to get into it. Here is a good article with basics from Blister labs
[QUOTE]. 3. Are there any PU membrane protectors (air permeable type) that ONLY go over the top of the mattress?
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Protectors are typically 5 or even 6 faced but quite thin whereas pads can be a little ticker and can alter the mattress comfort and feel Post #10 here has more information about mattress pads, protectors and the difference between them. Halfway through post #89 here there’s more about the pros and cons of different types of mattress protectors for those who want (or don’t) to affect the feel and performance of their mattress. You may wish to check out some of our members here who have good pads/protectors that they recommend to use. Also have a look at different types of mattress protectors here and here .
[QUOTE] 5. Has anyone ever seen a water resistant but not waterproof mattress pad that still allows high airflow but is not a thick wool type cover? [/QUOTE] ….
There are types of synthetic fibers (such as coolmax) that are specifically designed to draw moisture away from the skin and disperse it to the rest of the layer which can be effective as well.
As you are “concerned with issues related to water resistance and making sure the foam in this mattress has as much longevity as possible - body oils, light stains, mites, etc” you may want to consider natural fibers in your pad or protector. When you make your selection, I’d keep in mind that natural fibers are the most effective in terms of wicking and or storing moisture because synthetic fibers generally absorb moisture into the spaces, not the fiber itself. Artificial or “semi-synthetic” fibers (in between natural and synthetic) such as various types of cellulosic or rayon fibers (made from dissolved plant cellulose) are closer to natural fibers and do a good job of wicking moisture away from the body and ventilating. If you are considering placing the pad or protector between the latex and the pillowtop then the qualities of natural fibers are waisted as the layer is further away from the skin.
Generally, the materials, layers, and components of a sleeping system that are closer to the skin will have a bigger effect on airflow, moisture transport, and temperature regulation than materials, layers, and components that are further away from the skin. Also, you may want to keep in mind that some synthetic protectors may emit higher levels of VOCs. That being said there are many types of protectors… There are quite a few tradeoffs involved between how breathable they are … how much they will affect the feel of the mattress, the importance of natural materials, and of course cost. There is more about the choices and trade-offs involved and the amount of “protection” that may be important in post #2 here) and in post #5 here). Even though the post has some links to older products all other considerations still stand.
Phoenix