What do you mean by 'cottage cheese' hooves & what do you mean by 'natural shoeing'? Yes, recurring abscesses are a symptom of ill health of hooves and yes, even if they were healthy but the horse doesn't live/work enough on rough ground to become 'conditioned' to it, they're likely to need protection on that terrain.
My vote is also for boots over shoes, especially as I believe shoes are generally contraindicated for sick hooves. If you want to protect weak soles/frogs with conventional rims then yes, you do need pads also. Boots will provide the necessary protection & if further is needed you can use pads with them, but you only use them when necessary, so the feet can be cleaned, dry, trimmed etc as necessary rather being 'locked' into padded rims for 6 weeks or more.
What sort(Casey, you mean OLD Macs
) depends mostly on which ones fit him best. Other considerations are how much riding you'd be doing in them - eg. High profile boots such as Macs, Trails, Boas, etc can be problematic if you ride more than around 25 miles per week or ride, due to potential for rubbing. If your horse has odd feet, that will cut down on a few choices as some only come in pairs. How much maintenance your horse's hooves get and their form will be important considerations if you're thinking of Gloves, as they have no fastening system & require a pretty perfect fit. I wouldn't choose these without trying first. However, Easycare have just brought out a 'Backcountry Glove' which are effectively Glove shells with a high profile Trail upper, which doesn't require such perfect fitting. Whether or not you choose one of the Easycare line, if you get onto their site they have some good info on choosing the most appropriate boots.