Had an audit from those wonderful people back in the late 90"s or early 2000's, and they found online sales that were declared, reported, and I had no problem's with them over that. They do keep notes from audits and if you have been declaring your Ebay net income you should have no problem. It might help if where ever on the tax return that they ask for the nature of your business to state online sales including Ebay. I think at the moment they want to get those who have not been reporting any income. They may end up finding that there is more money to be paid when people start submitting receipts for the renovation tax credit and they start checking on contractors who have not been reporting net income or collecting GST/HST.
There are many ways that CRA uses to determine who to audit, not just Ebay gross sales. If a person has been buying a lot of stuff from a wholesaler CRA will often take a look at the books of the person that has been buying a lot of stuff. Living high and reporting low also gets CRA attention. The taxes are a pain in the butt, but its easier to comply than to evade them.