its usually just from wear and tear from lowering your car and putting extra stress on them, or spilling some kind of chemical on them that deteriorates the rubber...like brake cleaner or simple green or tranny fluid (i think they all deteriorate rubber... haha)

and the second question: you can buy new boots and repack them if your axle isnt shot (does it make a clicking noise when you make turns?) and they are cheap, but the labor is a lot. most people just replace the whole axle. (you can get a remanufactured axle at like pepboys or other stores like that) i replaced one of my axles on my accord (it was 100$) and installed it myself in autoshop, pretty simple if you have access to a lift or some jacks, and knowing what your doing is also a plus if you get it done, labor is prob gonna be around 100$ either way.