I don't think it is a criminal offence so it should not affect getting citizenship. You will be asked to pay back the benefit that you are not entitiled to, and next time when you apply for EI, your waiting period will be longer than 2 weeks. I tried to search on HRDC webpage to see the document, but their website changed so much I have no idea where they'd moved it. Your HRDC officer should be able to tell you.
I guess if you are only taking 1000 of not-entitled benefit, you shouldn't have been out of Canada for too long, eh? If the trip was on an emergency basis, you could explain that you didn't think about reporting at all because your mind was preoccupied on other issues. Admit that you are sorry and promise it won't happen again. It is better than saying you purposely did not report it. Neglecting to do something should be a lesser crime than abusing the system. I think.