I wouldn't worry about filling holes in joists either. It not gonna effect the integrity of the joist one iota. Now if a joist is bad, you'll either have to replace it or sister a joist alongside it. I wouldn't worry about trying to glue together a split joist either. Just replace or sister new one alongside it with deck screws and construction adhesive.
+1 If it's bad enough just replace it or scab to the side. If adding one beside the old one ,I would use full length and make sure it is secured to the structure just like the one you are replacing( like screwed into a seal plate and resting on a support). Use Liquid nails on the top of the joists to help secure the new decking and just use the longer nails.
