When I had a jazz bass I changed the pickguard from white to tort to black, and for some time I played it without a pickguard. I would probably do the same again if I ever got another one as changing the pickguard is so easy on a jazz.
If I buy a secondhand one and a previous owner had hacked up the pickup cavity, it would pee me off a lot, and if this was disclosed before the sale (as it should be) I wouldn't buy it.