Yes, he could file returns late for 06 and 07. Not sure you can still do it online though. And yes, if returns were required for those years and weren't done then when they find out he'll be fined.
I'm not sure exactly what the tax return form asks in respect of property income. It might ask when he began renting out in which case his choices will be to lie or tell the truth. If he tells the truth they may well come back and ask about earlier years. If he lies they probably won't but if he's ever found out then he'd have committed fraud by lying.
Presuming there genuinely wasn't any tax due for the previous years (and remember even a small profit should have seen tax assessed if he has another job) then there's no real point in lying about it. The consequences in tax terms are negligible. If there was no tax to pay then there's still no tax to pay. As said above there would be a penalty for late submission but no tax and consequently no interest either.
If he's genuinely worried about it go see an accountant. You might be surprised at the cost, it might not be much if it's pretty simple. If not then go ahead file this year as accurately as possible and wait to see what happens.