Can an indestructible creature die by a combination of damage and -X/-X effects?
No, he would be a 3/3 marked with 3 damage. This 3 damage would be 'lethal', but since he is indestructible, he is immune to such deaths. 


  702.12b A permanent with indestructible can’t be destroyed. Such permanents aren’t destroyed by lethal damage, and they ignore the state-based action that checks for lethal damage (see rule 704.5g).