as far as reusing joints or avoiding hem, I have seen both done. My suggestion would be, thoroughly inspect each mortise and if enough of them are in bad shape, then you should probably make new ones.
it's pretty common around here for old barns to be made out of even older ones. Often times they did cut totally new joints. In your case, cutting new ones seems to be the way to go, just make sure the timbers dont have too much wood hogged out to make them too weak.
