Hi reform,
You’ve probably read these already but just in case you’ve missed some of them (or for the sake of others that may read this) … most of your questions are answered in post #89 here about the pros and cons of different types of mattress protectors, post #2 here about mattress allergy or bed bug encasements, post #2 here about dust mite allergies, post #2 here about latex allergies, and post #2 here and the posts it links to about organic certifications.
I’ll add some comments here that hopefully will help fill in some of the blanks or “connect” some of the information together although which option is best for you will really be more about your preferences and the budget range you are most comfortable with than they will about making a "better/worse"choice.
The first thing I would decide is why “organic” is important to you since an organic certification is more about the farming methods used to grow an agricultural product than it is about “safety”. There are many non organic products that have been tested to standards such as Oeko-Tex standard 100 class 1 (safe for babies) that are just as “safe” as an organic product (I linked the Wikipedia article because the Oeko-Tex site is down at the moment). In the case of cotton I would personally prefer certified organic since cotton is among the most heavily sprayed crops on earth. In the case of wool there are many wool producers that use organic farming methods and don’t use any harsh chemicals in manufacturing their wool products but aren’t certified organic because of the extra costs involved that would have little benefit but would still have to be passed on to the consumer. This would be something like a food that you know is grown on a local farm that doesn’t use any pesticides and uses organic farming methods and that you know is just as healthy and “safe” (or perhaps even more so) than organic produce that is certified organic but costs less because they don’t wish to go through all the costly requirements to have their produce certified.
If “waterproof” is important to you then the “most waterproof” option would be one of the thin membrane types of protectors. They use a combination of fabrics that are bonded to a semi breathable synthetic membrane. While the membrane is synthetic (there is more information about the different types of membranes at the end of post #2 here) … they are safe and don’t offgass. The Naturepedic protector here is stretchy and uses GOTS certified organic cotton but like all the protectors of this type the membrane itself is a synthetic material (and not organic).
If a little less water resistance is OK with you then some of the wool/cotton combinations would be a good choice. They would be fine for all but the most “serious” accidents and would give you the time to remove the bedding in case of an accident before it has a chance to to through to the mattress. A “puddle pad” with a separate organic stretch cotton protector on top of it would likely be a little more water resistant than an all in one cotton/wool protector but thicker protectors or “systems” will also have a little more effect on the mattress than thinner protectors. This would probably be the preferred choice for those that prefer organic materials (or natural wool that is “just as natural” as organic wool) and don’t mind the extra cost.
If one or both of you have more serious allergies than it would be worthwhile to consider a 6 sided mattress encasement (along with other products that can help control dust mites such as a pillow encasement or foundation encasement, air purifiers etc) that can help control the dust mite population in your home. In this case I would use a more breathable encasement without a membrane because an encasement is meant to be left around the mattress on a more permanent basis and then you can use a 5 sided mattress protector on top of it that can be removed and washed on a more regular basis to keep your sleeping surface in a more hygienic condition.
If you either have bed bugs or are in a high risk area and you want to ensure that your mattress doesn’t become infested then I would use a mattress encasement that was meant for this specific purpose and had a locking zipper that doesn’t allow the bed bugs to escape. The better ones here have the membrane which are less breathable but this would be the tradeoff for bed bug protection. Since these also need to be left on the mattress permanently and not removed … I would also consider an additional 5 sided protector that can be removed and washed on a more regular basis but this wouldn’t need to be “waterproof” since the bed bug encasement would also be protecting the mattress from liquid accidents.
Between the cover that is around the mattress itself and any type of protector or sheets a latex contact allergy shouldn’t be an issue since you won’t be in contact with the latex with any of them.
Hopefully this will help you decide on the product or combination of protector products that would meet the criteria and preferences that are most important to you and your budget.
Phoenix